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File Rev. Age Author Last log entry
 Parent Directory        
README  1.1.1.1  16 years  efrank   import
test_cv.expected  1.1  14 years  efrank   Basic regression test on CV stuff at FIG API level (which underlies CGI).
get_evaluation_check_rast_new_vs_old.pl  1.1  12 years  bartels   compare old rast with development version
load_bbhs.pl  1.15  11 years  olson  *** empty log message ***
Consistency_Families.pm  1.1  11 years  bartels  *** empty log message ***
recompute_comparison.pl  1.1  11 years  bartels  *** empty log message ***
make_tf_equivalog_file.pl  1.1  11 years  bartels  *** empty log message ***
createTIGRfamSrc.pl  1.1  11 years  bartels  *** empty log message ***
set_not_private.pl  1.1  11 years  bartels  *** empty log message ***
get_synonyms_from_ach_for_id.pl  1.2  11 years  wilke  *** empty log message ***
expand_sims.pl  1.2  11 years  olson  *** empty log message ***
load_kegg.pl  1.9  12 years  dejongh  *** empty log message ***
add_assertions_of_function.pl  1.35  11 years  olson  *** empty log message ***
update_sims2.pl  1.4  11 years  olson  *** empty log message ***
alignment_to_html.pl  1.1  12 years  golsen  A command line script for converting fasta alignments to html. Accesses much of...
map_to_scaffold.pl  1.4  11 years  olson  Actually write out the changed entries.
build_anno_clearinghouse.pl  1.6  11 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
build_nr.pl  1.22  11 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
find_neighbors_by_sim.pl  1.4  11 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
auto_assign.pl  1.19  11 years  olson  Add -orgdir option to use FIGV and its indexed sims.
index_translation_files.c  1.5  11 years  golsen  Add J as a valid amino acid.
find_selenoproteins.pl  1.4  12 years  golsen  Add functions to reference selenoproteins, and add change the set slightly. Rep...
format_peg_dbs.pl  1.3  14 years  olson  Add license words.
index_sprout.pl  1.12  14 years  olson  Add license words.
export_subsystem_as_gff.pl  1.2  14 years  olson  Add license words.
run_start_predictions_for_all_subsystems.pl  1.4  14 years  olson  Add license words.
relevant_pchsG.pl  1.4  14 years  olson  Add license words.
compute_new_ids.pl  1.2  14 years  olson  Add license words.
build_nohit_fasta.pl  1.2  14 years  olson  Add license words.
count_bases.pl  1.2  14 years  olson  Add license words.
generate_Property_for_sprout.pl  1.6  14 years  olson  Add license words.
package_annotations.pl  1.9  14 years  olson  Add license words.
check_starts_for_pegs.pl  1.5  14 years  olson  Add license words.
fill_in_roles.pl  1.4  14 years  olson  Add license words.
update_sims.pl  1.13  14 years  olson  Add license words.
is_prokaryotic.pl  1.2  14 years  olson  Add license words.
get_class_examples.pl  1.2  14 years  olson  Add license words.
show_reconfig_cmd.pl  1.3  14 years  olson  Add license words.
split_sims.pl  1.3  14 years  olson  Add license words.
install_assignments.pl  1.7  14 years  olson  Add license words.
make_subsystems_from_clusters.pl  1.5  14 years  olson  Add license words.
sp2fasta.pl  1.2  14 years  olson  Add license words.
register_features_with_clearinghouse.pl  1.2  14 years  olson  Add license words.
changed_starts.pl  1.7  14 years  olson  Add license words.
order_sets.pl  1.3  14 years  olson  Add license words.
assign_towards_subsystems.pl  1.2  14 years  olson  Add license words.
filter_pegs_in_subsystems.pl  1.4  14 years  olson  Add license words.
extract_data_for_syncing_after_update.pl  1.6  14 years  olson  Add license words.
clean_subsystems.pl  1.2  14 years  olson  Add license words.
dna_seq.pl  1.2  14 years  olson  Add license words.
complete_genomes.pl  1.7  14 years  olson  Add license words.
load_links.pl  1.6  14 years  olson  Add license words.
build_alignments_for_subsystems.pl  1.4  14 years  olson  Add license words.
load_external_orgs.pl  1.3  14 years  olson  Add license words.
run_start_predictions_for_spreadsheet.pl  1.6  14 years  olson  Add license words.
align_fasta.pl  1.2  14 years  olson  Add license words.
check_lost_sims.pl  1.2  14 years  olson  Add license words.
sprout_search.pl  1.2  14 years  olson  Add license words.
init_peg_job_scheduler.pl  1.4  14 years  olson  Add license words.
make_attribute_index.pl  1.6  14 years  olson  Add license words.
get_nr_entries_without_sims.pl  1.4  14 years  olson  Add license words.
split_and_install_pchs.pl  1.2  14 years  olson  Add license words.
postprocess_computed_sims.pl  1.2  14 years  olson  Add license words.
generate_GenomeGroups_for_sprout.pl  1.3  14 years  olson  Add license words.
clustal2fasta.pl  1.2  14 years  olson  Add license words.
questionable_calls.pl  1.2  14 years  olson  Add license words.
select_genomes_for_sprout.pl  1.2  14 years  olson  Add license words.
synchronize_annotations_and_assignments.pl  1.2  14 years  olson  Add license words.
verify_pegs_in_tbl.pl  1.2  14 years  olson  Add license words.
blastn_seqs.pl  1.2  14 years  olson  Add license words.
cluster_by_sim.pl  1.2  14 years  olson  Add license words.
test_cv.pl  1.2  14 years  olson  Add license words.
bbhs.pl  1.7  14 years  olson  Add license words.
load_sets.pl  1.5  14 years  olson  Add license words.
compute_pins_and_clusters.pl  1.2  14 years  olson  Add license words.
db_xrefs_of.pl  1.4  14 years  olson  Add license words.
validate_subsystem.pl  1.2  14 years  olson  Add license words.
validate_genome_gff.pl  1.6  14 years  olson  Add license words.
external_calls.pl  1.2  14 years  olson  Add license words.
gff2Ontology.pl  1.4  14 years  olson  Add license words.
compute_simple_scores.pl  1.4  14 years  olson  Add license words.
make_sp_func_syn_dicts.pl  1.2  14 years  olson  Add license words.
pegs_in_conflict.pl  1.3  14 years  olson  Add license words.
break_scaffolds.pl  1.2  14 years  olson  Add license words.
insert_all.pl  1.2  14 years  olson  Add license words.
run_fc.pl  1.2  14 years  olson  Add license words.
check_alignment.pl  1.2  14 years  olson  Add license words.
apply_peg_changes_to_subsystem.pl  1.3  14 years  olson  Add license words.
load_pch_pins.pl  1.2  14 years  olson  Add license words.
test_generate_anno_gff.pl  1.3  14 years  olson  Add license words.
gather_attributes.pl  1.8  14 years  olson  Add license words.
get_pathways_for_EC.pl  1.2  14 years  olson  Add license words.
fix_annotations.pl  1.2  14 years  olson  Add license words.
ali_to_seq.pl  1.2  14 years  olson  Add license words.
display_tree.pl  1.4  14 years  olson  Add license words.
relabel_nodes.pl  1.2  14 years  olson  Add license words.
make_transferable_tarfiles.pl  1.3  14 years  olson  Add license words.
all_subsystems.pl  1.2  14 years  olson  Add license words.
check_for_unique_sims.pl  1.2  14 years  olson  Add license words.
blast_request.pl  1.2  14 years  olson  Add license words.
location_of.pl  1.2  14 years  olson  Add license words.
stop_services.pl  1.5  14 years  olson  Add license words.
process_sim_deletions_and_replacements.pl  1.3  14 years  olson  Add license words.
cat_spreadsheet.pl  1.2  14 years  olson  Add license words.
make_match_table.pl  1.2  14 years  olson  Add license words.
restrict_by_similarity.pl  1.4  14 years  olson  Add license words.
aliases_of.pl  1.6  14 years  olson  Add license words.
make_PHOBs_for_subsystems.pl  1.5  14 years  olson  Add license words.
lengths_of_contigs.pl  1.2  14 years  olson  Add license words.
check_peg_assignments.pl  1.3  14 years  olson  Add license words.
embl2gff_addmd5.py  1.2  14 years  olson  Add license words.
make_assignments_set.pl  1.3  14 years  olson  Add license words.
similar_to.pl  1.4  14 years  olson  Add license words.
initial_set.pl  1.2  14 years  olson  Add license words.
seed_job_scheduler.pl  1.3  14 years  olson  Add license words.
install_translation_rules.pl  1.3  14 years  olson  Add license words.
generate_pinned_homologs.pl  1.2  14 years  olson  Add license words.
apply_map.pl  1.2  14 years  olson  Add license words.
extract_DNA_sequence_from_object_for_start_predictions.pl  1.2  14 years  olson  Add license words.
alter_tbl.pl  1.4  14 years  olson  Add license words.
merge_translation_rules.pl  1.7  14 years  olson  Add license words.
extend_subsystem.pl  1.2  14 years  olson  Add license words.
map_sims.pl  1.5  14 years  olson  Add license words.
package_sims.pl  1.2  14 years  olson  Add license words.
fasta_to_phylip.pl  1.2  14 years  olson  Add license words.
install_lightweight_code.pl  1.2  14 years  olson  Add license words.
upstream.pl  1.3  14 years  olson  Add license words.
start_dbserver.pl  1.2  14 years  olson  Add license words.
cluster_by_bbhs.pl  1.2  14 years  olson  Add license words.
renumber_seed_dir.pl  1.2  14 years  olson  Add license words.
root_at.pl  1.2  14 years  olson  Add license words.
assign_to_hypo.pl  1.3  14 years  olson  Add license words.
import_external_sequences_step3.pl  1.5  14 years  olson  Add license words.
project.pl  1.2  14 years  olson  Add license words.
alias2fig.pl  1.2  14 years  olson  Add license words.
assign_with_no_sims.pl  1.2  14 years  olson  Add license words.
tabs2rel.pl  1.2  14 years  olson  Add license words.
is_archaeal.pl  1.2  14 years  olson  Add license words.
generate_Source_for_sprout.pl  1.2  14 years  olson  Add license words.
roles_in_subsystem.pl  1.2  14 years  olson  Add license words.
to_map_coords.pl  1.3  14 years  olson  Add license words.
peg_to_pdb.py  1.2  14 years  olson  Add license words.
extract_genes.pl  1.5  14 years  olson  Add license words.
blastp_pseq.pl  1.4  14 years  olson  Add license words.
clean_sims.pl  1.2  14 years  olson  Add license words.
dump_machine_state.pl  1.3  14 years  olson  Add license words.
condense_blast.pl  1.2  14 years  olson  Add license words.
make_fig_files.pl  1.3  14 years  olson  Add license words.
assign_synonym_ids.pl  1.2  14 years  olson  Add license words.
generate_genome_feature_tables_for_sprout.pl  1.16  14 years  olson  Add license words.
get_empty_ecs.pl  1.4  14 years  olson  Add license words.
make_sprout_upstream.pl  1.2  14 years  olson  Add license words.
parse_mart.py  1.6  14 years  olson  Add license words.
load_distances.pl  1.5  14 years  olson  Add license words.
make_maps_from_sub.py  1.5  14 years  olson  Add license words.
run_peg_job_worker.pl  1.4  14 years  olson  Add license words.
keep_only.pl  1.2  14 years  olson  Add license words.
add_close_genes.pl  1.2  14 years  olson  Add license words.
map_sims_for_bigfc.pl  1.2  14 years  olson  Add license words.
make_sp_org_domain_table.pl  1.2  14 years  olson  Add license words.
get_empty_ecs  1.3  14 years  olson  Add license words.
expand_multifunctional_roles.pl  1.3  14 years  olson  Add license words.
load_hugo.pl  1.6  14 years  olson  Add license words.
fix_eol.pl  1.2  14 years  olson  Add license words.
peg_to_subsystems.pl  1.3  14 years  olson  Add license words.
package_translation_rules.pl  1.2  14 years  olson  Add license words.
generate_gene_blocks.pl  1.3  14 years  olson  Add license words.
to_insert.pl  1.2  14 years  olson  Add license words.
where_does_seq_hit.pl  1.2  14 years  olson  Add license words.
make_phob_from_ids.pl  1.3  14 years  olson  Add license words.
init_dbserver.pl  1.3  14 years  olson  Add license words.
fill_in_cell.pl  1.2  14 years  olson  Add license words.
package_lightweight_code.pl  1.2  14 years  olson  Add license words.
genbank2gff3.pl  1.5  14 years  olson  Add license words.
paint_tree.pl  1.3  14 years  olson  Add license words.
make_sp_org_table.pl  1.2  14 years  olson  Add license words.
potentially_cotranscribed.pl  1.2  14 years  olson  Add license words.
p2p_sync_cron.pl  1.3  14 years  olson  Add license words.
possibly_truncated.pl  1.2  14 years  olson  Add license words.
fill_subsys.pl  1.5  14 years  olson  Add license words.
install_subsystems.pl  1.2  14 years  olson  Add license words.
delete_genomes_from_sims.pl  1.2  14 years  olson  Add license words.
set_to_relation.pl  1.2  14 years  olson  Add license words.
match_dna_to_aligned_prots.pl  1.4  14 years  olson  Add license words.
export_genome_as_gff.pl  1.6  14 years  olson  Add license words.
compare_tree_and_alignment.pl  1.2  14 years  olson  Add license words.
restore_annotations.pl  1.2  14 years  olson  Add license words.
check_nr_and_peg_synonyms.pl  1.2  14 years  olson  Add license words.
fid2dna.pl  1.2  14 years  olson  Add license words.
find_maximal_clusters.pl  1.2  14 years  olson  Add license words.
pull_sp_entries.pl  1.2  14 years  olson  Add license words.
best_hits.pl  1.2  14 years  olson  Add license words.
fusion_of.pl  1.2  14 years  olson  Add license words.
html_parser.py  1.2  14 years  olson  Add license words.
interval.pl  1.2  14 years  olson  Add license words.
trim_sequences.pl  1.6  14 years  olson  Add license words.
get_long_enough.pl  1.2  14 years  olson  Add license words.
make_sp_desc_with_org.pl  1.2  14 years  olson  Add license words.
check_fast_sims.pl  1.2  14 years  olson  Add license words.
pegs_in_subsystem.pl  1.5  14 years  olson  Add license words.
start_services.pl  1.12  14 years  olson  Add license words.
install_annotations.pl  1.4  14 years  olson  Add license words.
das_test.pl  1.2  14 years  olson  Add license words.
install_feature_updates.pl  1.2  14 years  olson  Add license words.
check_all_lost_sims.pl  1.2  14 years  olson  Add license words.
to_gg.pl  1.2  14 years  olson  Add license words.
is_eukaryotic.pl  1.2  14 years  olson  Add license words.
make_assignments_fit_initial_css.pl  1.4  14 years  olson  Add license words.
build_syn.pl  1.2  14 years  olson  Add license words.
extract_subset_from_sprout_data.pl  1.2  14 years  olson  Add license words.
load_literature.pl  1.3  14 years  olson  Add license words.
init_maps.pl  1.3  14 years  olson  Add license words.
add_assignments.pl  1.3  14 years  olson  Add license words.
generate_sprout_links.pl  1.2  14 years  olson  Add license words.
gi2fig.pl  1.3  14 years  olson  Add license words.
restrict_to_genomes.pl  1.3  14 years  olson  Add license words.
translate.pl  1.2  14 years  olson  Add license words.
make_spreadsheet_and_notes.pl  1.3  14 years  olson  Add license words.
restore_assignments.pl  1.2  14 years  olson  Add license words.
assign_synonym_ids_to_sims.pl  1.2  14 years  olson  Add license words.
make_sim_sets.pl  1.3  14 years  olson  Add license words.
get_best_set_of_genes_for_column.pl  1.3  14 years  olson  Add license words.
assign.pl  1.2  14 years  olson  Add license words.
reformat_dsim_dbs.pl  1.2  14 years  olson  Add license words.
p2p_daemon.pl  1.2  14 years  olson  Add license words.
generate_intergenic_blocks.pl  1.3  14 years  olson  Add license words.
package_raw_data_for_transplant.pl  1.2  14 years  olson  Add license words.
to_gids.pl  1.2  14 years  olson  Add license words.
extract_DNA_for_whole_ORFs.pl  1.3  14 years  olson  Add license words.
embl2gff.pl  1.20  14 years  olson  Add license words.
clustal_to_fasta.pl  1.2  14 years  olson  Add license words.
index_fasta.pl  1.2  14 years  olson  Add license words.
assign_to_sets.pl  1.5  14 years  olson  Add license words.
package_assignments.pl  1.8  14 years  olson  Add license words.
index_neighborhoods.pl  1.3  14 years  olson  Add license words.
filter_new_overlaps.pl  1.2  14 years  olson  Add license words.
subtree_of.pl  1.2  14 years  olson  Add license words.
bring_system_up_to_date.pl  1.2  14 years  olson  Add license words.
merge_annotations.pl  1.3  14 years  olson  Add license words.
index_contigs.pl  1.11  14 years  olson  Add license words.
genomes_of.pl  1.2  14 years  olson  Add license words.
build_access_sets.pl  1.2  14 years  olson  Add license words.
report_changes.pl  1.2  14 years  olson  Add license words.
expand_blast_table.pl  1.2  14 years  olson  Add license words.
compute_changed_ids_for_nrs.pl  1.4  14 years  olson  Add license words.
check_starts_for_peg_sets.pl  1.5  14 years  olson  Add license words.
is_bacterial.pl  1.2  14 years  olson  Add license words.
make_protein_sets.pl  1.4  14 years  olson  Add license words.
translation_of.pl  1.2  14 years  olson  Add license words.
splitup.pl  1.4  14 years  olson  Add license words.
generate_input_for_auto_assignments.pl  1.2  14 years  olson  Add license words.
check_tbl.pl  1.2  14 years  olson  Add license words.
uninstall.pl  1.2  14 years  olson  Add license words.
register_features_batch.pl  1.2  14 years  olson  Add license words.
make_annotations_for_sprout.pl  1.12  14 years  olson  Add license words.
make_transferable_chunks.pl  1.4  14 years  olson  Add license words.
package_code.pl  1.2  14 years  olson  Add license words.
dump_attributes.pl  1.2  14 years  olson  Add license words.
make_jpg.pl  1.2  14 years  olson  Add license words.
make_phob_from_seqs.pl  1.7  14 years  olson  Add license words.
uninstall.sims.pl  1.2  14 years  olson  Add license words.
make_sprout_bbhs.pl  1.2  14 years  olson  Add license words.
check_changes_in_organisms.pl  1.2  14 years  olson  Add license words.
pegs.pl  1.3  14 years  olson  Add license words.
check_sims_syntax.pl  1.3  14 years  olson  Add license words.
prep_viz.pl  1.2  14 years  olson  Add license words.
extract_data_to_keep.pl  1.5  14 years  olson  Add license words.
mark_nr.pl  1.2  14 years  olson  Add license words.
insert.pl  1.2  14 years  olson  Add license words.
backup_critical_data.pl  1.4  14 years  olson  Add license words.
reformat_fasta.pl  1.2  14 years  olson  Add license words.
make_rates.pl  1.2  14 years  olson  Add license words.
import_external_sequences_step1.pl  1.8  14 years  olson  Add license words.
fasta_for_hypo.pl  1.2  14 years  olson  Add license words.
pp.pl  1.3  14 years  olson  Add license words.
generate_max_clusters.pl  1.2  14 years  olson  Add license words.
put_directory_in_one_file.pl  1.2  14 years  olson  Add license words.
make_binary.pl  1.2  14 years  olson  Add license words.
build_excel_gene_table.pl  1.3  14 years  olson  Add license words.
generate_kernel_css.pl  1.5  14 years  olson  Add license words.
expand_transferred_chunks.pl  1.4  14 years  olson  Add license words.
p2p_sync_from_remote.pl  1.4  14 years  olson  Add license words.
make_calls.pl  1.4  14 years  olson  Add license words.
assign_synonym_ids_to_nr.pl  1.2  14 years  olson  Add license words.
representative_tree.pl  1.2  14 years  olson  Add license words.
relevant_PCHs.pl  1.3  14 years  olson  Add license words.
generate_subsys_tables_for_sprout.pl  1.8  14 years  olson  Add license words.
restore_translation_rules.pl  1.2  14 years  olson  Add license words.
build_exemplar_fasta.pl  1.3  14 years  olson  Add license words.
make_occ_counts.pl  1.2  14 years  olson  Add license words.
align_with_clustal.pl  1.8  14 years  olson  Add license words.
fix_ext_funcs.pl  1.2  14 years  olson  Add license words.
import_subsystems.pl  1.22  14 years  olson  Add license words.
fig_xmlrpc_server.pl  1.5  14 years  olson  Add license words.
install_code.pl  1.2  14 years  olson  Add license words.
load_local_maps.pl  1.3  14 years  olson  Add license words.
build_protein_families.pl  1.5  14 years  olson  Add license words.
generate_pin_caches.pl  1.5  14 years  olson  Add license words.
list_genomes.pl  1.2  14 years  olson  Add license words.
peg_to_name.pl  1.4  14 years  olson  Add license words.
distribute_attributes.pl  1.11  14 years  olson  Add license words.
rationalize_blast.pl  1.3  14 years  olson  Add license words.
load_chromosomal_clusters.pl  1.2  14 years  olson  Add license words.
install_features_batch.pl  1.1  11 years  olson  Add new script to install a batch of genomid.tbl / genomeid.fasta files. Initial...
sims_all.pl  1.5  12 years  overbeek  Added '-no_redo_blast' switch. -- /gdp
make_close_strain_data.pl  1.13  12 years  overbeek  Added 'noEdoBLAST' flag. -- /gdp
add_rbs_data_for_start_predictions.pl  1.3  12 years  gdpusch  Added FIGV support. -- /gdp
order_corrections_for_start_predictions.pl  1.5  12 years  gdpusch  Added FIGV support. -- /gdp
add_sim_data_for_start_predictions.pl  1.8  12 years  gdpusch  Added FIGV support. -- /gdp
get_sims_for_start_predictions.pl  1.5  12 years  gdpusch  Added FIGV support. -- /gdp
predict_starts.pl  1.8  12 years  gdpusch  Added FIGV support. -- /gdp
start_data_for_set_of_pegs.pl  1.6  12 years  gdpusch  Added FIGV support. -- /gdp
add_start_data_for_start_predictions.pl  1.4  12 years  gdpusch  Added FIGV support. -- /gdp
get_potential_starts_for_start_predictions.pl  1.3  12 years  gdpusch  Added FIGV support. -- /gdp
make_calls_for_start_predictions.pl  1.4  12 years  gdpusch  Added FIGV support. -- /gdp
cache_comparison_data.pl  1.9  11 years  parrello  Added a use Carp.
assess_gene_call_quality.pl  1.10  12 years  overbeek  Added brute-force "-no_fatal" hack to convert FATALs to WARNINGs. -- /gdp
predict_scenarios.pl  1.2  12 years  formsma  Added code to automatically run 'run_scenarios All' if it hasn't been run. These...
bayes_expected_start_scores.pl  1.3  12 years  overbeek  Added comments to expalin logic. -- gdp
find_neighbors_using_figfams.pl  1.8  11 years  gdpusch  Added comments, divide-by-zero protection, and removed an ill-thought-out hand-o...
add_structured_english.pl  1.4  11 years  disz  Added escape arg to structured engkish
SpanishInquisition.pl  1.1  11 years  parrello  Added for testing the Confess method.
renumber_features.pl  1.11  11 years  gdpusch  Added option to print out ID map. -- /gdp
make_SBML_model.pl  1.5  12 years  formsma  Added reaction ATPSYN for manual since KEGG doesn't have it - Kevin
remove_embedded_pegs.pl  1.17  11 years  gdpusch  Added setting of VERBOSE from metafile. -- /gdp
remove_rna_overlaps.pl  1.10  11 years  gdpusch  Added setting of VERBOSE from metafile. -- /gdp
filter_overlaps.pl  1.5  13 years  overbeek  Added some more diagnosting lines. -- /gdp
get_fasta_for_tbl_entries.pl  1.9  12 years  gdpusch  Added support for multi-exon locations. -- /gdp
to_genbank.pl  1.4  12 years  gdpusch  Added support for multiple contig files. -- /gdp
run_glimmer2.pl  1.7  12 years  gdpusch  Added support for multiple genetic codes. -- /gdp
run_model_generation.pl  1.16  12 years  formsma  Added timestamp in GMT to the readme that is generated - Kevin
peg2pubmed.pl  1.1  13 years  hwang  Added two scripts that will generate pubmed files
genomes_with_essentiality_data.pl  1.1  13 years  redwards  Adding tools to handle essentiality data for Sveta
verify_genome_directory.pl  1.36  11 years  gdpusch  Augmented genetic code table to translate ambiguous codons that _could_ be STOPs...
create_sims_btree.pl  1.1  14 years  olson  BTREE-index versions of these. Experimental still.
load_coupling_btree.pl  1.1  14 years  olson  BTREE-index versions of these. Experimental still.
load_bbhs_btree.pl  1.1  14 years  olson  BTREE-index versions of these. Experimental still.
to_prodom.pl  1.6  13 years  hwang  Change url for prodom's post
load_attributes.pl  1.45  12 years  parrello  Changed POD format for better compatability with Wiki.
Packager.pl  1.7  12 years  parrello  Changed POD format for better compatability with Wiki.
find_model_information.pl  1.6  12 years  formsma  Changed logic on input prediction for dealing with biomass compounds - Kevin
load_abstract_coupling.pl  1.3  14 years  parrello  Changed to use a single-character delimiter (for compatability with PostGRES).
diff_tbls.pl  1.1  14 years  overbeek  Computes difference betwween two tbl files. -- /gdp
insert_prot_into_tree.pl  1.14  12 years  golsen  Continuing the update of tree packages and programs
TestLocations.pl  1.8  11 years  parrello  Converted to use new name for Contrain method.
find_protein_homologs.pl  1.1  12 years  golsen  Debugging and adding support of all the NCBI genetic codes.
md5.c  1.3  14 years  olson  Doh, put proper comments in for C code.
fasta_cksum.c  1.4  14 years  olson  Doh, put proper comments in for C code.
index_sims_file.c  1.3  14 years  olson  Doh, put proper comments in for C code.
fastasize.c  1.3  14 years  olson  Doh, put proper comments in for C code.
load_ec_names.pl  1.5  14 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
Simple.pl  1.4  14 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
test_parse_gff.pl  1.3  14 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
get_id_mapping_for_list_of_IDs.pl  1.1  11 years  wilke  Draft version for id mapping
collect_related_sequences.pl  1.3  12 years  golsen  Encapsulate all of the SEED-dependent functions in the perl module. It should st...
genome_peg_dna.pl  1.3  12 years  golsen  Extensive modifications to allow more options, and handle large genomes by not r...
get_journals_for_frole.pl  1.1  12 years  hwang  Files to get journal information from PubMed
find_genes_based_on_neighbors.pl  1.22  11 years  gdpusch  Final clean-up. -- /gdp
promote_orfs_to_pegs.pl  1.13  11 years  gdpusch  Final clean-up. -- /gdp
find_genes_in_families.pl  1.20  11 years  gdpusch  Final clean-up. -- /gdp
compute_genome_counts.pl  1.16  13 years  golsen  Fix bug introduced in trying to trim "root" from taxonomies.
exclude_genomes.pl  1.3  11 years  parrello  Fixed a POD error.
import_similarity_bundle.pl  1.3  11 years  parrello  Fixed a POD error.
backup_subsystems.pl  1.3  11 years  parrello  Fixed a POD error.
check_model.pl  1.6  11 years  parrello  Fixed a POD error.
pull_orfs.pl  1.4  13 years  overbeek  Fixed case-sensitivity bug. -- /gdp
feature_length_histogram.pl  1.3  12 years  gdpusch  Fixed duplicated ID bug, plus minor cosmetic changes. -- /gdp
find_gaps.pl  1.8  12 years  gdpusch  Fixed error in lower boundary constraint. -- /gdp
make_genome_dir_for_close.pl  1.9  11 years  gdpusch  Fixed handling of spliced loci. -- /gdp
find_essential_reactions.pl  1.2  12 years  formsma  Fixed incorrect filehandle. Tested Good - Kevin
run_glimmer3.pl  1.9  11 years  gdpusch  Fixed neglected linear topology swicth. -- /gdp
make_close.pl  1.7  13 years  parrello  Fixed obsolete form of boundaries_of.
map_pegs.pl  1.3  13 years  parrello  Fixed obsolete form of boundaries_of.
trace.pl  1.3  11 years  parrello  Fixed so that the destination is not case-sensitive.
pull_fasta_entries.pl  1.7  13 years  overbeek  Fixed switch-parsing bug. -- /gdp
WikiMaker.pl  1.5  11 years  parrello  Fixed unlinking to be more robust.
features_with_role.pl  1.1  12 years  golsen  Function to get the ids or sequences of features that match a given role. Uses F...
make_reaction_network.pl  1.1  12 years  olson  Hope College modifications.
compare_scenarios.pl  1.4  12 years  dejongh  Hope College updates
load_sims.pl  1.10  13 years  olson  If we are loading unmapped files (as generated by make_close -no-map and make_s...
index_feature_dir_fasta.pl  1.1  11 years  olson  Index scripts for FIGV accleration.
index_figv_annos.pl  1.1  11 years  olson  Index scripts for FIGV accleration.
fix_invalid_fasta.pl  1.1  12 years  redwards  Initial release of programs to check and fix valid fasta format
validate_fasta.pl  1.1  12 years  redwards  Initial release of programs to check and fix valid fasta format
install_anticipated_functions.pl  1.3  11 years  olson  Introduct &FIG::get_figfams_data()
compare_figfam_release_results.pl  1.4  11 years  olson  Introduct &FIG::get_figfams_data()
check_figfams.pl  1.6  11 years  olson  Introduct &FIG::get_figfams_data()
meta.pl  1.9  11 years  olson  Introduct &FIG::get_figfams_data()
test_figfam_placement_into_families.pl  1.9  11 years  olson  Introduct &FIG::get_figfams_data()
sync_new_system.pl  1.6  14 years  golsen  Just adding a newline at end of file to make repository match my working copy. ...
gff2seed.pl  1.28  12 years  redwards  Just adding comments and docs
build_figfam_pssm_db.pl  1.2  12 years  gdpusch  Major modifications to &load_family_ids()
load_dlits.pl  1.5  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
export_dlits.pl  1.2  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
compute_extra_dlit_data.pl  1.4  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
compare_tbls.pl  1.5  13 years  overbeek  Minor change to output. -- /gdp
get_dna.pl  1.6  12 years  gdpusch  Minor cosmetic change. -- /gdp
test_figfam_FF_peg.pl  1.3  11 years  olson  Missed one of the figfamdata fixes.
remove_clustered_pchs2.pl  1.1  12 years  olson  Missing scripts.
remove_sims_not_in_nr.pl  1.1  12 years  olson  Missing scripts.
maint-remove-obsolete-aliases.pl  1.1  12 years  olson  Missing scripts.
remove_clustered_pchs3.pl  1.1  12 years  olson  Missing scripts.
compute_genome_similarity.pl  1.1  12 years  olson  Missing scripts.
register_genome_with_clearinghouse.pl  1.1  12 years  olson  Missing scripts.
index-pegsyn.pl  1.1  12 years  olson  Missing scripts.
check_fasta_for_dups.pl  1.1  12 years  olson  Missing scripts.
add_to_alignment.pl  1.6  12 years  golsen  Modifications to control ordering of sequences in representative sets and in seq...
representative_sequences.pl  1.4  12 years  golsen  Modifications to control ordering of sequences in representative sets and in seq...
build_initial_objects_for_start_predictions.pl  1.12  12 years  gdpusch  Modified to also work on new genomes using "FIGV.". -- /gdp
reformat_contigs.pl  1.16  11 years  gdpusch  Modified to split on runs of ambigs, not just N or X. -- /gdp
assign_to_unchanged.pl  1.3  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
fig_net.pl  1.4  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
generate_similarities.pl  1.3  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
conditionally_assign.pl  1.4  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
fig_rpc.pl  1.4  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
fig.pl  1.133  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
make_protein_weights_and_rates.pl  1.2  12 years  golsen  Moving some tree building tools into packages.
add_prots_to_tree.pl  1.1  12 years  golsen  New script for adding proteins to an existing tree.
ListLits.pl  1.1  11 years  parrello  New script to count literature references for NMPDR.
make_overlap_report.pl  1.20  12 years  gdpusch  No longer complains about split loci. -- /gdp
explore_subsys_pmid.pl  1.5  12 years  hwang  PEG information is no longer stored in the file. Parsing of the file in this scr...
extract_fasta_idmap.pl  1.1  13 years  overbeek  RAE: Adding FigKernelScripts/extract_fasta_idmap.pl
nmpdr2gff.pl  1.1  13 years  overbeek  RAE: Changes to gff3 files for NMPDR and adding nmpdr2gff for creating the files...
read_write_excel.pl  1.1  13 years  overbeek  RAE: Initial release of a simple script to read and write excel files to allow e...
score_ifcs.pl  1.4  13 years  overbeek  RAE: More direct and indirect functional coupling scores
delete_all_attribute_files.pl  1.2  13 years  overbeek  RAE: New delete attribute files to remove all files. maybe this will work
make_fam_tabs.pl  1.5  14 years  overbeek  RAE: Protein Families interface and construction
iedb.pl  1.10  13 years  overbeek  RAE: bugger, correcting the array dereferencing
score_ifcs_mcauliffe.pl  1.2  13 years  overbeek  RAE: correcting indirect functional coupling score
load_pirsf.pl  1.14  13 years  overbeek  RAE: correcting load_pirsf not recognizing a firewall
load_protein_families.pl  1.9  14 years  overbeek  RAE: extending protein families
seed2pir.pl  1.3  13 years  overbeek  RAE: moving PIRSF to links
score_dfcs.pl  1.3  13 years  overbeek  RAE: removing the header that should not be in the source
load_coupling.pl  1.9  13 years  olson  Remove debugging.
make_peg_map_from_tbl.pl  1.2  11 years  gdpusch  Removed hard-coded regexps that failed to handle multi-exon loci. -- /gdp
LigandCleanup.pl  1.2  11 years  parrello  Removed obsolete use clases.
TransactFeatures.pl  1.20  11 years  parrello  Removed obsolete use clause.
NMPDRAnalysis.pl  1.5  11 years  parrello  Removed obsolete use clauses.
OneShotAttributeAdder.pl  1.2  11 years  parrello  Removed obsolete use clauses.
purge_fasta.pl  1.1  13 years  overbeek  Removes duplicate entries from fasta file. -- /gdp
purge_tbl.pl  1.1  13 years  overbeek  Removes duplicate entries from tbl file. -- /gdp
make_proml_tree.pl  1.6  12 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
make_proml_tree_0.pl  1.1  12 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
gff2tab.pl  1.5  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
sequence_length_histogram.pl  1.4  12 years  gdpusch  Rewrote counting of DNA characters (-get_dna option). -- /gdp
rapid_propagation.pl  1.69  11 years  olson  Rollup of RAST release changes.
compute_pchs_from_sims.pl  1.2  12 years  olson  Rollup of changes for the new RAST install.
build_nr_sources.pl  1.14  12 years  olson  Rollup of various rast-related changes.
process_new_sims.pl  1.6  12 years  olson  Rollup of various rast-related changes.
show_structured_english.pl  1.1  11 years  disz  Ross's code to generate annotations for NCBI
init_FIG.pl  1.9  14 years  olson  SQLite support.
map-nr-ids-to-ncbi-std.pl  1.1  11 years  olson  Script to map IDs in a SEED NR into forms acceptable to the indexed NCBI fasta p...
Makefile.cprogs  1.2  12 years  olson  Support compilation of nap.c
compute_translation_MD5.c  1.1  11 years  golsen  Support of MD5 hash codes for SEED translations.
find_special_proteins.pl  1.4  11 years  gdpusch  Suppress writing "called_by" and "special_pegs" when "-keep" is selected. -- /gd...
PickGeneBoundariesTest.pl  1.1  11 years  parrello  Test script for backfill.
to_arabidopsis.pl  1.1  12 years  hwang  This script parses arabidopsis.org to get the AT aliases output
run_model_generation_all.pl  1.1  12 years  formsma  This script will generate models for all complete genomes in the seed. - Kevin
align_with_clustal_2.pl  1.4  12 years  golsen  Trivial format change.
seed2genbank.pl  1.3  12 years  olson  Tweak outptu file handling, expand '%g' into genome name. Allow diret output int...
bielefeld_tarfile_to_seed.pl  1.7  13 years  overbeek  Tweaked usage msg. -- /gdp
update-caches.pl  1.1  12 years  olson  Update SEED caches.
make_kegg_files.pl  1.5  13 years  overbeek  Update parsing of NAME field to reflect change in source file. -- /gdp
get_ev_codes.pl  1.15  11 years  parrello  Updated comments to mention the replacement scripts.
ev_code_cron.pl  1.16  11 years  parrello  Updated comments to mention the replacement scripts.
run_scenarios.pl  1.3  12 years  formsma  Updated error statements to be correct - Kevin
find_missing_lib_inputs.pl  1.5  12 years  formsma  Updated error statements. Added compound name printing. - Kevin
make_MPS_model.pl  1.6  12 years  formsma  Updated some logic for the sink reactions. Fixes flux issues - Kevin
make_fasta_btree.pl  1.1  12 years  olson  Utility for creating btree access for fasta files.
sort_and_split_bbhs.pl  1.5  12 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
all_bbhs.pl  1.16  12 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
connections_between.pl  1.6  12 years  olson  add FIGV support, use strict
analyze_scenario_connections.pl  1.3  12 years  olson  add FIGV support.
generate_GO_attributes.pl  1.1  13 years  overbeek  add GO attribute genertation
sketch_tree.pl  1.2  13 years  overbeek  add ability to insert sequences into a tree
add_to_subsystems.pl  1.1  13 years  overbeek  add add_to_subsystems
best_tree_using_proml_on_cluster.pl  1.1  12 years  overbeek  add best_tree_using_proml_on_cluster
find_poss_fs.pl  1.1  12 years  overbeek  add code to fix frameshifts in a genome
check_for_possible_mobile_elements.pl  1.1  12 years  overbeek  add code to search for mobile elements
index_subsystems.pl  1.10  13 years  overbeek  add comments to functions
runclustalw.pl  1.4  12 years  overbeek  add computation of alignments to building FIGFAMS
filter_figfams.pl  1.2  12 years  overbeek  add computation of alignments to building FIGFAMS
figfam.pl  1.22  11 years  overbeek  add connections between FIGfams and structures
ff.pl  1.6  11 years  overbeek  add connections between FIGfams and structures
make_timestamps.pl  1.4  13 years  overbeek  add initial version of FIGO.pm - OO services
tips_of.pl  1.3  13 years  overbeek  add insert_prot_into_tree, a new way to insert proteins into a tree
get_figfam_funcs.pl  1.1  13 years  overbeek  add install_anticipated_functions and some FIGfam tracking stuff
trimmed_kernel_alignment.pl  1.1  12 years  overbeek  add last round of phylogeny tools
COPYING.TXT  1.1  14 years  olson  add license file
reps_and_close.pl  1.2  12 years  overbeek  add make_trimmed_alignment_from_ids
Makefile  1.21  11 years  olson  add md5 modl
new_versions_of_features.pl  1.1  13 years  overbeek  add new_versions_of_features
install_new_coupling_data.pl  1.3  12 years  olson  add option to install from a jobdir
potentially_missed_assignments.pl  1.1  13 years  overbeek  add potentially_missed_assignments
make_partition_reps_worker.pl  1.1  11 years  overbeek  add program orf computing representative sequences for the partitions
make_partition_repsP.pl  1.1  11 years  overbeek  add program orf computing representative sequences for the partitions
install_partition_reps.pl  1.1  11 years  overbeek  add program to install partition representatives in FigfamsData
make_parallel_proml_run.pl  1.2  13 years  overbeek  add rates to phylogeny stuff
to_structured_english.pl  1.1  11 years  overbeek  add routine to build structured english rendering of evidence codes
flattened_to_fasta.pl  1.1  14 years  overbeek  add some minor utilities to flatten/unflatten fasta files
flatten_fasta.pl  1.1  14 years  overbeek  add some minor utilities to flatten/unflatten fasta files
close_connections.pl  1.2  12 years  overbeek  add strip comments argument on function_of
merge_families.pl  1.3  12 years  overbeek  add strip comments argument on function_of
ali_tree.pl  1.4  12 years  overbeek  add strip comments argument on function_of
gff2ncbitab.pl  1.3  11 years  olson  add swissprot
insert_into_a_tree.pl  1.5  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
uproot.pl  1.1  13 years  overbeek  add uproot
align_seqs.pl  1.1  12 years  overbeek  add utilities for computing alignments
order_seqs_on_length.pl  1.1  12 years  overbeek  add utilities for computing alignments
compute_sim_chunk.pl  1.3  13 years  olson  add working-on-chunk support
make_Phobius_attributes.pl  1.2  12 years  mkubal  added date as 2nd argument
make_PFAM_HMM_derived_attributes.pl  1.2  12 years  mkubal  added date as 2nd argument
aclh.pl  1.11  11 years  paarmann  added new parameter to dump contribs
get_evaluation_check.pl  1.3  12 years  bartels  added option -a for showing pegs that do not match via blast
find_subsys.pl  1.3  11 years  overbeek  allow loose matching in rapid_propagation
load_peg_mapping.pl  1.9  12 years  olson  bah. it's all fine to ask for a table name on the command line, but it helps if ...
compareMR.pl  1.1  12 years  overbeek  basic stuff for comparing metabolic reconstructions
blast_pdb_against_nr_on_tla.pl  1.1  12 years  mkubal  blast pdb against nr
index_annotations.pl  1.11  12 years  olson  bugfix
salvage_annotations.pl  1.6  13 years  olson  bugfix.
make_uniprot_corr.pl  1.2  11 years  overbeek  build uniprot correspondence
subsys2pubmed.pl  1.4  12 years  hwang  change script to add new attribute after each subsystem versus after all subsyst...
make_SignalP_attributes.pl  1.2  12 years  mkubal  changed ; to :: for key separator
make_CELLO_and_TMPRED_attributes.pl  1.2  12 years  mkubal  changed ; to :: for key separator
make_ncbi_files.pl  1.4  12 years  wilke  changed check for existing directories
make_sp_uni_files.pl  1.4  12 years  wilke  changed check for input and output directory the directories may exists, so don'...
run_model_generation_v3.pl  1.2  12 years  mkubal  changed ouput to model_files.tgz
extract_genomes.pl  1.38  13 years  overbeek  changes to support dynamic sims and updates
adjacent.pl  1.3  12 years  redwards  changing chop to chomp
prepare_metagenome_files_for_ftp.pl  1.3  12 years  mkubal  checks for PUBLIC file
generate_ilits.pl  1.2  11 years  overbeek  code relating to dlit/ilit maintenance
generate_ilit_ev_codes.pl  1.4  11 years  overbeek  code relating to dlit/ilit maintenance
generate_partitions_worker.pl  1.1  11 years  overbeek  code to generate partitions for FIGfams
index_nr.pl  1.2  12 years  olson  compute length btree also
index_sims.pl  1.11  12 years  olson  compute_pchs_from_sims.pl
make_sim_tab.pl  1.8  12 years  olson  compute_pchs_from_sims.pl
compute_mw_and_pi_with_BioPerl.pl  1.1  12 years  mkubal  computes mw and pi for all pegs in complete genomes
correct_gff_missing_contigs.pl  1.5  12 years  redwards  correcting a weird error
bring_tree_up_to_ali.pl  1.5  12 years  overbeek  debugged version of bring_tree_up_to_ali
make_neigh_joining_tree.pl  1.8  12 years  overbeek  debugged version of bring_tree_up_to_ali
evaluate_quality_of_trees.pl  1.4  12 years  overbeek  debugged version of bring_tree_up_to_ali
make_indexes.pl  1.15  12 years  olson  disable attribute indexing.
uni_lit_to_dlits.pl  1.1  11 years  overbeek  dlit support
compute_ev_code_attributes.pl  1.2  11 years  overbeek  do not include cluster-based subsystems in forming evidence codes
get_ss_connections.pl  1.11  12 years  olson  don't crash on missing SS
update_lineage.pl  1.3  12 years  wilke  draft version to update FIG taxonomy entries
run_flux_optimization.pl  1.3  12 years  mkubal  error checking
make_figfams.pl  1.3  13 years  overbeek  families.2c should get current function - not family function
fast_blastp.pl  1.1  11 years  overbeek  fast_blastp is a tool to support rapid similarity estimates using FIGfam partiti...
run_remote_Phobius_for_fasta.pl  1.1  12 years  mkubal  fasta file as input
extract_sp_links.pl  1.3  13 years  olson  fix -h error
check_all_subsystems.pl  1.10  11 years  overbeek  fix bug in check_all_subsystems
myjoin.pl  1.1  13 years  overbeek  fix building FigFamData
check_and_extend_all_subsystems.pl  1.7  13 years  overbeek  fix call to rapid_subsystem_extension in check_and_extend_all_subsystems
split_and_trim_sequences.pl  1.14  12 years  overbeek  fix problem when repeats occur
remove_clustered_pchs.pl  1.10  13 years  overbeek  fix rfemove_clustered_PCHs to count correctly
to_org_specific.pl  1.4  13 years  hwang  fix syntax error
load_features.pl  1.24  11 years  olson  fix tmp file name.
install-data.pl  1.8  12 years  olson  fix to dvd data installer
compute_potential_fusions.pl  1.12  14 years  overbeek  fix to fusions
make_PDB_attributes.pl  1.2  12 years  mkubal  fix to score format
make_CDD_attributes.pl  1.2  12 years  mkubal  fix to score format
make_IPR_PFAM_GO_attributes.pl  1.3  12 years  mkubal  fix to score format
make_PROSITE_PIR_PRODOM_attributes.pl  1.3  12 years  mkubal  fix to score format
index_contig_files.c  1.5  14 years  olson  fix to work on 64-bit linux
backfill_gaps.pl  1.17  11 years  olson  fix typo
make_MFA_tool_input.pl  1.1  11 years  mkubal  fixed formatting errors
split_clean_unclean_families.pl  1.4  13 years  overbeek  fixes for splitting families into clean/unclean
export_ACH_resolution_DB.pl  1.2  11 years  overbeek  fixes relating to comments
assign_to_close_strains.pl  1.10  13 years  overbeek  fixes to Assignments.pm
function_of.pl  1.5  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
partition_prots.pl  1.2  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
functionally_coupled.pl  1.7  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
package_subsystems.pl  1.5  14 years  overbeek  fixes to deleted_features, replace_features_with, etc
same_subsys.pl  1.1  14 years  overbeek  fixes to extract_genomes
are_close.pl  1.1  14 years  overbeek  fixes to extract_genomes
initialize_alignments_for_subsystems.pl  1.2  14 years  overbeek  fixes to extract_genomes, salvage_subsystem_rows and initialize_alignments_for_s...
fc_figfams.pl  1.2  12 years  overbeek  fixes to fc_figfams
rapid_subsystem_inference.pl  1.13  11 years  overbeek  fixes to inference of -1 variants
load_ACH_resolution_DB.pl  1.4  11 years  overbeek  fixes to quotemeta characters in loading comments
rep_genomes.pl  1.1  13 years  overbeek  fixes to representative tree generation and added rep_genomes
salvage_subsystem_rows.pl  1.6  14 years  overbeek  fixes to salvage code
salvage_master_annotations.pl  1.3  14 years  overbeek  fixes to salvage code
pegs_in_subsystems.pl  1.5  13 years  overbeek  fixes to usable_subsystem
make_close_strain_family_tabs.pl  1.2  13 years  overbeek  fixes to wseekly statistics
find_bad_conflicts.pl  1.1  13 years  overbeek  fixes to wseekly statistics
make_proposed_assignments_for_consistency.pl  1.4  13 years  overbeek  fixes to wseekly statistics
check_model_v2.pl  1.1  12 years  mkubal  for Model Repository Oct 2007
find_missing_lib_inputs_v2.pl  1.1  12 years  mkubal  for Model Repository Oct 2007
find_model_information_v2.pl  1.1  12 years  mkubal  for Model Repository Oct 2007
make_MPS_model_v2.pl  1.1  12 years  mkubal  for Model Repository Oct 2007
run_remote_Phobius_for_genome.pl  1.1  12 years  mkubal  for single genome
test_Observation.pl  1.1  12 years  mkubal  for testing
run_remote_Phobius_for_genome_for_RAST.pl  1.1  12 years  mkubal  for use with RAST server
prepare_metagenome_files_for_download.pl  1.4  11 years  mkubal  full loop
mg_user_id_to_unique.pl  1.2  11 years  mkubal  full loop
cluster_objects.pl  1.3  12 years  overbeek  generalize cluster_objects
ensure_genome_registration.pl  1.1  12 years  olson  generate feature registration stuff
get_taxid_journals.pl  1.1  12 years  hwang  get journals from PMC using taxide
make_assertions_from_uploads.pl  1.3  11 years  overbeek  get rid of debugging message
track_figfams.pl  1.2  13 years  overbeek  get rid of diagnostics in track_figfams
get_NCBI_genome_attributes.pl  1.1  11 years  arodri7  get_NCBI_genome_attributes searches the NCBI internet sites for genome attribute...
get_translations.pl  1.3  13 years  overbeek  get_translations can take PEG ids from STDIN
seed2gff.pl  1.36  11 years  redwards  getting rid of need for strain info
same_figfam.pl  1.2  12 years  overbeek  handle bad input in same_figfam
check_hope_info.pl  1.3  11 years  dejongh  hope script
check_for_scenario_reachability.pl  1.2  11 years  mkubal  identifiesspecific missing input substrate
parse_genbank.pl  1.17  11 years  wilke  ids have prefixes now , e.g for locus tags locus|ID
metagenome2genbank.pl  1.4  11 years  mkubal  includes data from meta.xml
index_translations.pl  1.20  11 years  overbeek  increase bound on maximum number of sequences
index_translations_MD5.pl  1.2  11 years  overbeek  increase bound on maximum number of sequences
indirect_functional_coupling.pl  1.5  13 years  overbeek  indirect functional coupling should not be from a PEG to itself
indirect_functional_coupling_mcauliffe.pl  1.5  13 years  overbeek  indirect functional coupling should not be from a PEG to itself
blastn_chunks.pl  1.3  12 years  overbeek  initial, undebugged version of edit_feature.cgi
load_locks.pl  1.1  13 years  overbeek  introduce locks on features to block assignments
add_attributes_from_file.pl  1.1  12 years  redwards  just a simple attribute loader
assess_completeness.pl  1.8  13 years  overbeek  leave master: on subsystem_curator
score_dfcs_mcauliffe.pl  1.5  13 years  overbeek  limit decimal positions in score
update_nr_cycle.pl  1.6  13 years  overbeek  load ext org table on update_nr_cycle
build_new_figfam_release.pl  1.4  11 years  arodri7  made default procedure the ross hack for new families
pubmed_gene2peg.pl  1.2  13 years  redwards  making sure gene id is right
genbank2fasta.pl  1.1  11 years  paarmann  minimal version to extract fasta from genbank
check_subs_and_split_warnings.pl  1.3  11 years  overbeek  minor fix to handle deleted subsystems
make_peg_maps.pl  1.3  14 years  overbeek  minor fixes
trim_alignment.pl  1.2  12 years  overbeek  minor fixes
export_similarity_request.pl  1.3  13 years  overbeek  minor fixes to assignment for close strains
curator_of.pl  1.1  13 years  overbeek  minor fixes to assignment for close strains
get_subsystem_properties.pl  1.1  12 years  overbeek  minor modifications to get subsystems statistics
rel2tabs.pl  1.1  13 years  overbeek  minor tools
boot_cluster_seed.pl  1.5  14 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
compute_dbdir_checksum.pl  1.3  14 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
find_model_cofactors.pl  1.6  12 years  mkubal  more error checking
install_rast_batch.pl  1.4  12 years  olson  more fixes
index_anno_clearinghouse.pl  1.3  12 years  olson  multiple id support, build fixes
index_pins.pl  1.3  13 years  olson  new pin indexer
make_reduce_sims_index.pl  1.1  12 years  olson  new script
make_peg_maps_from_fasta.pl  1.1  12 years  olson  new scripts
index-pegsyn2.pl  1.1  11 years  olson  new version of pegsyn indexer that presorts data before inserting into the btree...
split_assignments_based_on_subsystems.pl  1.1  13 years  overbeek  next version of the STAG code
compute_mw_and_pi.pl  1.2  12 years  mkubal  one genome at a time
make_subsys_based_families.pl  1.13  11 years  overbeek  only nonaux roles
make_FigFamsData.pl  1.4  13 years  overbeek  order generated FIGfams
order_figfams.pl  1.1  13 years  overbeek  order_figfams
make_interpro_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_Ontology_database.pl  1.3  11 years  mkubal  provides usage when no argument given
make_go_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_prosite_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_cdd_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_pir_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_pdb_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_pfam_ontology.pl  1.4  11 years  mkubal  provides usage when no argument given
load_go.pl  1.2  13 years  overbeek  put in the fr2go stuff
update_fr2go.pl  1.1  13 years  overbeek  put in the fr2go stuff
seed_run_job.pl  1.4  13 years  olson  readonly fixes; seed-run-job update to run from input file
seed_run_task.pl  1.2  13 years  olson  readonly fixes; seed-run-job update to run from input file
test_placement.pl  1.1  12 years  overbeek  redone FIGfam stuff
check_peg_placement.pl  1.1  12 years  overbeek  redone FIGfam stuff
gff_statistics.pl  1.1  13 years  redwards  releasing gff statistics
make_external_sequence_data.pl  1.2  13 years  olson  remove .pl from invocations
blast2gff.pl  1.21  12 years  redwards  removing error messages
summarize_taxonomy_by_blast.pl  1.9  11 years  redwards  removing fatal error if 0 or 1 hits
build_partition_index.pl  1.1  11 years  overbeek  return empty list of failure to open FIFfam
make_trimmed_alignment_from_ids.pl  1.13  11 years  overbeek  return empty list of failure to open FIFfam
find_neighbors.pl  1.30  11 years  overbeek  return empty list of failure to open FIFfam
flip_sims.pl  1.7  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
reformat_sims.pl  1.8  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
reformat_timelogic_sims.pl  1.2  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
reduce_sims.pl  1.11  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
compute_contig_md5.pl  1.4  12 years  olson  rollup of metagenome server changes
run_remote_Phobius_for_genomes.pl  1.1  12 years  mkubal  run for all complete prok genomes
submit_to_iprscan_on_biocluster.pl  1.1  12 years  mkubal  run iprscan on cluster
run_remote_PHOBIOUS.pl  1.1  12 years  mkubal  runs Phobius computation for given geneome
aclh_reload_contrib.pl  1.1  11 years  paarmann  script to reload the contrib dbs of the aclh
update_taxonomies.pl  1.8  13 years  overbeek  set longer gap between accessing NCBI
filter_tbl_overlaps.pl  1.10  13 years  overbeek  set up find_neighbors to handle existing genomes
correct_frameshifts.pl  1.13  11 years  overbeek  shift position of correct_frameshifts in rapid_propagation pipeline
split_by_genome.pl  1.1  13 years  overbeek  split_by_genome can be used to split a score or BBH file
check_subsystems.pl  1.7  12 years  overbeek  strip comments on functions for subsystem checking
subsys_info.pl  1.1  11 years  overbeek  subsys_info is subsystem information for Verionika
generate_dlit_ev_codes.pl  1.5  11 years  overbeek  switching to new ilidt/dlit stuff
compute_CELLO_and_TMPRED.pl  1.2  12 years  mkubal  test for dir exist
submit_genome_to_signalP.pl  1.2  12 years  mkubal  test for dir exist
submit_genome_to_rpsblast_against_CDD_on_biocluster.pl  1.2  12 years  mkubal  test for dir exist
get_journals_for_org.pl  1.1  12 years  hwang  this script is the backend to get journals using taxonomy id or name. This calls...
load_close.pl  1.9  12 years  overbeek  tighten length constraints for figfam matching
direct_functional_coupling.pl  1.4  12 years  overbeek  tighten length constraints for figfam matching
compute_pins.pl  1.4  11 years  olson  undo bogus commit
initialize_ann_and_ev.pl  1.3  11 years  olson  undo bogus commit
connect_PDB_to_FIGfams_worker.pl  1.1  11 years  arodri7  update changes
make_figfam_tree.pl  1.1  11 years  arodri7  update changes
propagate_subsys_changes_to_figfams.pl  1.9  11 years  arodri7  update changes
figfam_quality_control.pl  1.7  11 years  arodri7  update changes
install_partitions.pl  1.3  11 years  arodri7  update changes
connect_PDB_to_FIGfams.pl  1.1  11 years  arodri7  update changes
test_figfam_peg.pl  1.6  11 years  arodri7  update changes
figfam_subsystems.pl  1.1  11 years  arodri7  update changes
figfam_size_distribution.pl  1.1  11 years  arodri7  update changes
assign_using_ff.pl  1.3  11 years  arodri7  update changes
initialize_figfams.pl  1.7  11 years  arodri7  update changes
make_figfam_tree_worker.pl  1.1  11 years  arodri7  update changes
submit_ff_test.pl  1.4  11 years  arodri7  update changes
update_FIGfams.pl  1.10  11 years  arodri7  update changes
get_pubmed_journals.pl  1.5  12 years  hwang  update comment that this is for peg curation
possible_frameshifts.pl  1.1  12 years  overbeek  update possible_frameshifts
sims_between.pl  1.7  12 years  overbeek  updates on close connections
run_find_subsys_against_all_genomes.pl  1.2  12 years  overbeek  updates to computation of VCs
load_id_correspondence.pl  1.3  11 years  olson  updates to the load_id_correspondence loader and searching code.
update_uniq_id_data.pl  1.7  12 years  olson  use function_of_quick
crc64.py  1.1  11 years  mkubal  uses for mapping of interpro downlaod to pegs
build_alignments_from_spreadsheet.pl  1.7  13 years  redwards  using is_environmental
check_sims_basic.pl  1.8  13 years  redwards  using is_environmental instead of seven 9s
fig_specific_sequences.pl  1.3  13 years  redwards  using is_environmental instead of seven 9s
extend_subsys.pl  1.7  13 years  redwards  using is_environmental instead of seven 9s
make_model_spreadsheets.pl  1.1  12 years  mkubal  v1
parse_uniparc.pl  1.1  12 years  mkubal  v1
compute_crc64_for_all_pegs.pl  1.1  12 years  mkubal  v1
add_figbar_and_genome_attributes.pl  1.1  12 years  mkubal  v1
run_HMM_search_on_timelogic.pl  1.1  12 years  mkubal  version 1.0
rebuild_global_chromosomal_clusters.pl  1.2  12 years  overbeek  version of rebuild_global_chromosomal_clusters that works
generate_partitionsP.pl  1.3  11 years  overbeek  write concatenated output to STDOUT
BuildCodonUsageExchAndLoadFiles.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_build_alignments.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_close_strains.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_collapse_repeats.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_create_SNP_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_filter_unique.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_first_pass.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_gather_mapped_objects.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_get_close_strain_annotations.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_get_repeat_dna.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_layout.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_make_conn.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_make_contig_index.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_make_unique_kmers.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_merge_estimates.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_predict_features_based_on_refs.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_ref_vs_ref.pl (dead) No revisions exist on mgrast_rel_2008_0919
CSA_second_pass.pl (dead) No revisions exist on mgrast_rel_2008_0919
CS_build_fasta_for_phylogeny.pl (dead) No revisions exist on mgrast_rel_2008_0919
CS_compute_coupling.pl (dead) No revisions exist on mgrast_rel_2008_0919
CheckCELfiles.R (dead) No revisions exist on mgrast_rel_2008_0919
ComputeSproutCouplings.pl (dead) No revisions exist on mgrast_rel_2008_0919
ComputeSproutSequences.pl (dead) No revisions exist on mgrast_rel_2008_0919
EcoliRMA.R (dead) No revisions exist on mgrast_rel_2008_0919
EmergencyMapFlipper.pl (dead) No revisions exist on mgrast_rel_2008_0919
EmergencySubsystemFix.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_build_ff_indexes.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_build_updated_FF.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_compare_tests.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_compare_to_anno3.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_compute_relationships_for_genera.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_create_binary_kmers.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_create_binary_relationships.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_families_in_subsystems.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_genome_group_pipeline.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_get_oligos.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_get_oligos2.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_get_prot_gs_oligos.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_get_prots.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_install_kmers.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_load_memcache.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_load_oligo_index.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_make_FF_index.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_make_family_vector.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_make_subsys_based_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_merge_and_build_kmers.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_merge_families_based_on_genus_groups.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_merge_oligos.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_pull_extreme_FF_members.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_run_tests.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_split_fams_by_size.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_update_FIGfams.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_usable_motifs.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_usable_motifs2.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_validate_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_xx.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB2_xy.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_assemble_translations.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_build_ff_indexes.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_build_ff_oligos.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_build_otu_oligos.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_build_updated_FF.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_cleanup_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_compare_tests.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_construct_assigned_functions.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_create_binary_kmers.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_families_to_fasta.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_get_gs_oligos.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_get_oligos.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_get_recent_annotations.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_load_oligo_index.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_make_subsys_based_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_make_subsys_based_families_2.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_merge_and_build_kmers.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_merge_families_by_kmers.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_package_figfams.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_run_parallel_usable_motifs.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_run_tests.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_set_figfam_functions.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_update_FIGfams.pl (dead) No revisions exist on mgrast_rel_2008_0919
FFB3_usable_motifs.pl (dead) No revisions exist on mgrast_rel_2008_0919
FIGMODELscheduler.pl (dead) No revisions exist on mgrast_rel_2008_0919
GTO_to_PGF_genome_stats.pl (dead) No revisions exist on mgrast_rel_2008_0919
GeneSet_P_Values.R (dead) No revisions exist on mgrast_rel_2008_0919
GenomeTypeObject.t (dead) No revisions exist on mgrast_rel_2008_0919
KeyDump.pl (dead) No revisions exist on mgrast_rel_2008_0919
MFADriver.pl (dead) No revisions exist on mgrast_rel_2008_0919
ModelDriver.pl (dead) No revisions exist on mgrast_rel_2008_0919
Pipeline.R (dead) No revisions exist on mgrast_rel_2008_0919
RunRMA.R (dead) No revisions exist on mgrast_rel_2008_0919
RunRMA_SIF_format.R (dead) No revisions exist on mgrast_rel_2008_0919
SStest.pl (dead) No revisions exist on mgrast_rel_2008_0919
ShewanellaRMA.R (dead) No revisions exist on mgrast_rel_2008_0919
SplitGeneSets.R (dead) No revisions exist on mgrast_rel_2008_0919
SwissProtJSON_to_loadfile.pl (dead) No revisions exist on mgrast_rel_2008_0919
SwissProtXML_to_JSON.pl (dead) No revisions exist on mgrast_rel_2008_0919
Tracer.pl (dead) No revisions exist on mgrast_rel_2008_0919
WebAppBackend.pl (dead) No revisions exist on mgrast_rel_2008_0919
accumulate_pegs_to_scenario_paths.pl (dead) No revisions exist on mgrast_rel_2008_0919
add_assertions_of_function (dead) No revisions exist on mgrast_rel_2008_0919
add_dlits.pl (dead) No revisions exist on mgrast_rel_2008_0919
add_phage_from_rast.sh (dead) No revisions exist on mgrast_rel_2008_0919
align_with_clustal (dead) No revisions exist on mgrast_rel_2008_0919
analyze_kmer_assignments.pl (dead) No revisions exist on mgrast_rel_2008_0919
analyze_loose_sets.pl (dead) No revisions exist on mgrast_rel_2008_0919
analyze_package_logs.pl (dead) No revisions exist on mgrast_rel_2008_0919
annotate-ss-with-pattyfams.pl (dead) No revisions exist on mgrast_rel_2008_0919
annotation_counts.pl (dead) No revisions exist on mgrast_rel_2008_0919
apply_annotations.pl (dead) No revisions exist on mgrast_rel_2008_0919
apply_automatic_subsystem_updates.pl (dead) No revisions exist on mgrast_rel_2008_0919
apply_map (dead) No revisions exist on mgrast_rel_2008_0919
assemble_selected.pl (dead) No revisions exist on mgrast_rel_2008_0919
assess_genome_quality.pl (dead) No revisions exist on mgrast_rel_2008_0919
assess_quality.pl (dead) No revisions exist on mgrast_rel_2008_0919
assign (dead) No revisions exist on mgrast_rel_2008_0919
assign_figfam.pl (dead) No revisions exist on mgrast_rel_2008_0919
assign_to_dna_using_kmers.pl (dead) No revisions exist on mgrast_rel_2008_0919
assign_to_hypo (dead) No revisions exist on mgrast_rel_2008_0919
assign_to_sets (dead) No revisions exist on mgrast_rel_2008_0919
assign_using_dna_server.pl (dead) No revisions exist on mgrast_rel_2008_0919
assign_using_dna_server_simple.pl (dead) No revisions exist on mgrast_rel_2008_0919
assign_using_dna_server_standalone.pl (dead) No revisions exist on mgrast_rel_2008_0919
assign_using_ff_original.pl (dead) No revisions exist on mgrast_rel_2008_0919
assign_using_ff_parallel.pl (dead) No revisions exist on mgrast_rel_2008_0919
assign_using_ff_server.pl (dead) No revisions exist on mgrast_rel_2008_0919
assign_using_ff_server_simple.pl (dead) No revisions exist on mgrast_rel_2008_0919
assign_using_ff_server_standalone.pl (dead) No revisions exist on mgrast_rel_2008_0919
assign_using_kmers.pl (dead) No revisions exist on mgrast_rel_2008_0919
assign_with_no_sims (dead) No revisions exist on mgrast_rel_2008_0919
assigned_functions_from_rast.pl (dead) No revisions exist on mgrast_rel_2008_0919
at.pl (dead) No revisions exist on mgrast_rel_2008_0919
auto_assign (dead) No revisions exist on mgrast_rel_2008_0919
batch_of_bbhs.pl (dead) No revisions exist on mgrast_rel_2008_0919
bbh_synteny.pl (dead) No revisions exist on mgrast_rel_2008_0919
blastP.pl (dead) No revisions exist on mgrast_rel_2008_0919
blast_request (dead) No revisions exist on mgrast_rel_2008_0919
blastn_seqs (dead) No revisions exist on mgrast_rel_2008_0919
blastp_pseq (dead) No revisions exist on mgrast_rel_2008_0919
blocked_by.pl (dead) No revisions exist on mgrast_rel_2008_0919
br_evaluate_properties.pl (dead) No revisions exist on mgrast_rel_2008_0919
break_scaffolds (dead) No revisions exist on mgrast_rel_2008_0919
bring_system_up_to_date (dead) No revisions exist on mgrast_rel_2008_0919
build_PGs_for_OTUs.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_SEED_nr.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_access_sets (dead) No revisions exist on mgrast_rel_2008_0919
build_aligns_and_trees_for_seqs.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_all_prok_seqs.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_contigs_blastdb.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_dnaseq_blastdb.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_dtr_distro.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_excel_gene_table (dead) No revisions exist on mgrast_rel_2008_0919
build_exemplar_fasta (dead) No revisions exist on mgrast_rel_2008_0919
build_family_dir_from_genera.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_nap_alignments.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_nohit_fasta (dead) No revisions exist on mgrast_rel_2008_0919
build_nr (dead) No revisions exist on mgrast_rel_2008_0919
build_nr_md5.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_prok_nonff_fasta.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_pssm_db.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_sample_sigs.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_sas_distro.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_sas_distro_from_cvs.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_sets_from_clusters.pl (dead) No revisions exist on mgrast_rel_2008_0919
build_solid_set.pl (dead) No revisions exist on mgrast_rel_2008_0919
call_coregulated_clusters_on_chromosome.pl (dead) No revisions exist on mgrast_rel_2008_0919
call_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
call_genome_using_glimmer.pl (dead) No revisions exist on mgrast_rel_2008_0919
cat_spreadsheet (dead) No revisions exist on mgrast_rel_2008_0919
check_all_lost_sims (dead) No revisions exist on mgrast_rel_2008_0919
check_changes_in_organisms (dead) No revisions exist on mgrast_rel_2008_0919
check_consistency_of_rectangles.pl (dead) No revisions exist on mgrast_rel_2008_0919
check_consistency_of_sample.pl (dead) No revisions exist on mgrast_rel_2008_0919
check_fast_sims (dead) No revisions exist on mgrast_rel_2008_0919
check_for_new_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
check_for_unique_sims (dead) No revisions exist on mgrast_rel_2008_0919
check_genomes_by_ribo_proteins.pl (dead) No revisions exist on mgrast_rel_2008_0919
check_gto.pl (dead) No revisions exist on mgrast_rel_2008_0919
check_lost_sims (dead) No revisions exist on mgrast_rel_2008_0919
check_rast.pl (dead) No revisions exist on mgrast_rel_2008_0919
check_sims_for_added_genome.pl (dead) No revisions exist on mgrast_rel_2008_0919
check_start_for_peg.pl (dead) No revisions exist on mgrast_rel_2008_0919
check_tbl (dead) No revisions exist on mgrast_rel_2008_0919
clean_bad_contigs.pl (dead) No revisions exist on mgrast_rel_2008_0919
clean_sims (dead) No revisions exist on mgrast_rel_2008_0919
cleanup_figfams_updates.pl (dead) No revisions exist on mgrast_rel_2008_0919
cluster_exp.pl (dead) No revisions exist on mgrast_rel_2008_0919
cluster_objects (dead) No revisions exist on mgrast_rel_2008_0919
clustered_hypotheticals.pl (dead) No revisions exist on mgrast_rel_2008_0919
codon_counts_x_and_p.c (dead) No revisions exist on mgrast_rel_2008_0919
codon_freq_eval_2.c (dead) No revisions exist on mgrast_rel_2008_0919
collate_reads.pl (dead) No revisions exist on mgrast_rel_2008_0919
compare_annotation_sets.pl (dead) No revisions exist on mgrast_rel_2008_0919
compare_ec_gary_table.pl (dead) No revisions exist on mgrast_rel_2008_0919
compare_gto_assigned_roles.pl (dead) No revisions exist on mgrast_rel_2008_0919
compare_gto_called_CDSs.pl (dead) No revisions exist on mgrast_rel_2008_0919
compare_two_sets_of_calls.pl (dead) No revisions exist on mgrast_rel_2008_0919
complement_fasta.c (dead) No revisions exist on mgrast_rel_2008_0919
compute_PCA_for_metagenomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
compute_PCA_with_metagenomes_as_variables.pl (dead) No revisions exist on mgrast_rel_2008_0919
compute_PSEED_reconstructions.pl (dead) No revisions exist on mgrast_rel_2008_0919
compute_atomic_regulons.pl (dead) No revisions exist on mgrast_rel_2008_0919
compute_atomic_regulons_for_dir.pl (dead) No revisions exist on mgrast_rel_2008_0919
compute_changed_ids_for_nrs (dead) No revisions exist on mgrast_rel_2008_0919
compute_fasta_lengths.pl (dead) No revisions exist on mgrast_rel_2008_0919
compute_figfam_assignments.pl (dead) No revisions exist on mgrast_rel_2008_0919
compute_pc.pl (dead) No revisions exist on mgrast_rel_2008_0919
compute_potential_fusions (dead) No revisions exist on mgrast_rel_2008_0919
compute_ribo_ratio.pl (dead) No revisions exist on mgrast_rel_2008_0919
compute_ribo_ratio_by_function.pl (dead) No revisions exist on mgrast_rel_2008_0919
compute_stats_for_kmer_hits.pl (dead) No revisions exist on mgrast_rel_2008_0919
condense_blast (dead) No revisions exist on mgrast_rel_2008_0919
condense_kmer_output.pl (dead) No revisions exist on mgrast_rel_2008_0919
convert-blast-to-m8.pl (dead) No revisions exist on mgrast_rel_2008_0919
convert_tbl_files.pl (dead) No revisions exist on mgrast_rel_2008_0919
core_PGF_stats.pl (dead) No revisions exist on mgrast_rel_2008_0919
corr_build_connections.pl (dead) No revisions exist on mgrast_rel_2008_0919
create-new-page.pl (dead) No revisions exist on mgrast_rel_2008_0919
create_ff_covering_skeleton.pl (dead) No revisions exist on mgrast_rel_2008_0919
create_partitions.pl (dead) No revisions exist on mgrast_rel_2008_0919
cripple_gto.pl (dead) No revisions exist on mgrast_rel_2008_0919
cs_adjacency_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
daily.pl (dead) No revisions exist on mgrast_rel_2008_0919
delete_fids_from_orgdir.pl (dead) No revisions exist on mgrast_rel_2008_0919
delete_functions_for_nonextent_ff.pl (dead) No revisions exist on mgrast_rel_2008_0919
delete_genomes_from_sims (dead) No revisions exist on mgrast_rel_2008_0919
difference_between_two_databases.pl (dead) No revisions exist on mgrast_rel_2008_0919
dose_response_extract.pl (dead) No revisions exist on mgrast_rel_2008_0919
dose_response_ic50.pl (dead) No revisions exist on mgrast_rel_2008_0919
dose_response_sheets.pl (dead) No revisions exist on mgrast_rel_2008_0919
dp.pl (dead) No revisions exist on mgrast_rel_2008_0919
dump_ss_classification.pl (dead) No revisions exist on mgrast_rel_2008_0919
duplicate_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
ec_compare_sib.pl (dead) No revisions exist on mgrast_rel_2008_0919
estimated_fabric.pl (dead) No revisions exist on mgrast_rel_2008_0919
eval_matrix.py (dead) No revisions exist on mgrast_rel_2008_0919
evaluate_annotation_consistency.pl (dead) No revisions exist on mgrast_rel_2008_0919
evaluate_properties.pl (dead) No revisions exist on mgrast_rel_2008_0919
ex_add_conditions.pl (dead) No revisions exist on mgrast_rel_2008_0919
ex_adjust_peg_on_off.pl (dead) No revisions exist on mgrast_rel_2008_0919
ex_compute_pccs.pl (dead) No revisions exist on mgrast_rel_2008_0919
ex_fillout_ar_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
ex_get_adjacency_based_estimates.pl (dead) No revisions exist on mgrast_rel_2008_0919
ex_get_subsystem_based_estimates.pl (dead) No revisions exist on mgrast_rel_2008_0919
ex_make_initial_atomic_regulons.pl (dead) No revisions exist on mgrast_rel_2008_0919
ex_make_on_off_calls.pl (dead) No revisions exist on mgrast_rel_2008_0919
ex_pipeline_ross.pl (dead) No revisions exist on mgrast_rel_2008_0919
ex_rare_ar_and_pegs.pl (dead) No revisions exist on mgrast_rel_2008_0919
ex_set_on_off_for_atomic_regulons.pl (dead) No revisions exist on mgrast_rel_2008_0919
ex_split_atomic_regulons.pl (dead) No revisions exist on mgrast_rel_2008_0919
exec-cgi.pl (dead) No revisions exist on mgrast_rel_2008_0919
exp_pc_compute.pl (dead) No revisions exist on mgrast_rel_2008_0919
expand_blast_table (dead) No revisions exist on mgrast_rel_2008_0919
export_all_viruses.pl (dead) No revisions exist on mgrast_rel_2008_0919
export_phage_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
export_subsystem.pl (dead) No revisions exist on mgrast_rel_2008_0919
extract_genomes (dead) No revisions exist on mgrast_rel_2008_0919
extract_genomes_from_samples.pl (dead) No revisions exist on mgrast_rel_2008_0919
extract_halo_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
extract_metagene_contigs.pl (dead) No revisions exist on mgrast_rel_2008_0919
fabric_vec.pl (dead) No revisions exist on mgrast_rel_2008_0919
fast_grep.pl (dead) No revisions exist on mgrast_rel_2008_0919
fast_project.pl (dead) No revisions exist on mgrast_rel_2008_0919
fast_project_ref_to_GTO.pl (dead) No revisions exist on mgrast_rel_2008_0919
fasta2phylip.pl (dead) No revisions exist on mgrast_rel_2008_0919
fasta_dna.pl (dead) No revisions exist on mgrast_rel_2008_0919
fasta_for_hypo (dead) No revisions exist on mgrast_rel_2008_0919
fasta_size.pl (dead) No revisions exist on mgrast_rel_2008_0919
fc.pl (dead) No revisions exist on mgrast_rel_2008_0919
fetch_models_for_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
fetch_seed_gto.pl (dead) No revisions exist on mgrast_rel_2008_0919
fig (dead) No revisions exist on mgrast_rel_2008_0919
fig_net (dead) No revisions exist on mgrast_rel_2008_0919
filter_and_merge_gene_sets.pl (dead) No revisions exist on mgrast_rel_2008_0919
filter_codon_counts.pl (dead) No revisions exist on mgrast_rel_2008_0919
filter_on_known.pl (dead) No revisions exist on mgrast_rel_2008_0919
filter_trunc_and_fs.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_IS.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_RNA_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_SEED_SSU_rRNA_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_approx_neigh.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_bad_contigs.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_bidir_best_hits.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_close_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_genes_based_on_kmers.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_genes_based_on_neighbors_par.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_miscalled_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_missing_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_more_instances_for_veronika.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_new_annotations.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_poss_errs.pl (dead) No revisions exist on mgrast_rel_2008_0919
find_rnas.pl (dead) No revisions exist on mgrast_rel_2008_0919
fix_eol (dead) No revisions exist on mgrast_rel_2008_0919
fix_sprout_annotation_relations.pl (dead) No revisions exist on mgrast_rel_2008_0919
flatten_attribute_files.pl (dead) No revisions exist on mgrast_rel_2008_0919
flatten_erdb_xml.pl (dead) No revisions exist on mgrast_rel_2008_0919
form_clusters.pl (dead) No revisions exist on mgrast_rel_2008_0919
format_partition_dbs.pl (dead) No revisions exist on mgrast_rel_2008_0919
fq_to_fa.pl (dead) No revisions exist on mgrast_rel_2008_0919
freqs_2_dists.pl (dead) No revisions exist on mgrast_rel_2008_0919
freqs_2_nj_tree.pl (dead) No revisions exist on mgrast_rel_2008_0919
gather_genome_info.pl (dead) No revisions exist on mgrast_rel_2008_0919
gather_pg_sets.pl (dead) No revisions exist on mgrast_rel_2008_0919
gd_tree.pl (dead) No revisions exist on mgrast_rel_2008_0919
generate_SproutData.pl (dead) No revisions exist on mgrast_rel_2008_0919
generate_all_bbhs.pl (dead) No revisions exist on mgrast_rel_2008_0919
generate_clusters.pl (dead) No revisions exist on mgrast_rel_2008_0919
generate_comparisons.pl (dead) No revisions exist on mgrast_rel_2008_0919
generate_input_for_auto_assignments (dead) No revisions exist on mgrast_rel_2008_0919
generate_kegg_map_ec_tables.pl (dead) No revisions exist on mgrast_rel_2008_0919
generate_kmer_peg_rel.pl (dead) No revisions exist on mgrast_rel_2008_0919
generate_picked.pl (dead) No revisions exist on mgrast_rel_2008_0919
generate_pinned_homologs (dead) No revisions exist on mgrast_rel_2008_0919
generate_prolog_facts.pl (dead) No revisions exist on mgrast_rel_2008_0919
generate_similarities (dead) No revisions exist on mgrast_rel_2008_0919
genome_set.t (dead) No revisions exist on mgrast_rel_2008_0919
get_FIGfams_SS_NMPDR_stats.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_ON_probes.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_PATRIC_AMR_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_PATRIC_AMR_genome_list.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_PSEED_assignment_updates.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_all.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_all_annotations.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_all_dlits.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_close_pegs.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_close_pegs_kmer_memcache.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_core_PGFs.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_coupling_values.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_dlit_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_dna (dead) No revisions exist on mgrast_rel_2008_0919
get_exemplars_as_needed.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_fam_corr.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_fam_rel.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_families_1.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_families_2.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_families_3.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_families_4.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_families_final.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_families_kmcl.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_fasta_for_tbl_entries (dead) No revisions exist on mgrast_rel_2008_0919
get_genome_object_from_seed.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_genomes_from_ncbi.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_list_of_genomes_to_delete.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_merged_families_2.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_merged_families_3.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_needed_corr.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_neighbors_and_corr_to_ref.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_pairs.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_peg_md5_func_subsystem.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_recent_annotations.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_rid_of_small_or_too_many_per_FF.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_rna_features_for_calling_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_translations_for_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
get_unique_kmers_for_rnaseq.pl (dead) No revisions exist on mgrast_rel_2008_0919
gjocodonlib.c (dead) No revisions exist on mgrast_rel_2008_0919
gjocodonlib.h (dead) No revisions exist on mgrast_rel_2008_0919
gjoseqio.c (dead) No revisions exist on mgrast_rel_2008_0919
gjoseqio.h (dead) No revisions exist on mgrast_rel_2008_0919
gjoseqlib.c (dead) No revisions exist on mgrast_rel_2008_0919
gjoseqlib.h (dead) No revisions exist on mgrast_rel_2008_0919
glue_tbl_to_metabolic_reconstruction.pl (dead) No revisions exist on mgrast_rel_2008_0919
gset-initdb.pl (dead) No revisions exist on mgrast_rel_2008_0919
gto_complete_check.pl (dead) No revisions exist on mgrast_rel_2008_0919
gto_crisprs.pl (dead) No revisions exist on mgrast_rel_2008_0919
gto_to_tbl.pl (dead) No revisions exist on mgrast_rel_2008_0919
harvest_genomes_from_samples.pl (dead) No revisions exist on mgrast_rel_2008_0919
ic50_compare.pl (dead) No revisions exist on mgrast_rel_2008_0919
ic50_extract.pl (dead) No revisions exist on mgrast_rel_2008_0919
identify_organism.pl (dead) No revisions exist on mgrast_rel_2008_0919
index_annotations (dead) No revisions exist on mgrast_rel_2008_0919
index_contigs (dead) No revisions exist on mgrast_rel_2008_0919
index_genome.pl (dead) No revisions exist on mgrast_rel_2008_0919
index_neighborhoods (dead) No revisions exist on mgrast_rel_2008_0919
index_sims (dead) No revisions exist on mgrast_rel_2008_0919
index_translations (dead) No revisions exist on mgrast_rel_2008_0919
init_FIG (dead) No revisions exist on mgrast_rel_2008_0919
install_annotations (dead) No revisions exist on mgrast_rel_2008_0919
install_assignments (dead) No revisions exist on mgrast_rel_2008_0919
install_code (dead) No revisions exist on mgrast_rel_2008_0919
install_lightweight_code (dead) No revisions exist on mgrast_rel_2008_0919
install_translation_rules (dead) No revisions exist on mgrast_rel_2008_0919
janaka_pipeline.pl (dead) No revisions exist on mgrast_rel_2008_0919
jgi_data_merge.pl (dead) No revisions exist on mgrast_rel_2008_0919
just_inconsistent_sets.pl (dead) No revisions exist on mgrast_rel_2008_0919
k-class-PSEED-kc.pl (dead) No revisions exist on mgrast_rel_2008_0919
k-class-adaboost-classify.pl (dead) No revisions exist on mgrast_rel_2008_0919
k-class-adaboost-matrix-parallel.pl (dead) No revisions exist on mgrast_rel_2008_0919
k-class-adaboost.pl (dead) No revisions exist on mgrast_rel_2008_0919
k-class-get-adaboost-tree-tips.pl (dead) No revisions exist on mgrast_rel_2008_0919
k-class-get-bork-universals.pl (dead) No revisions exist on mgrast_rel_2008_0919
k-class-kc.pl (dead) No revisions exist on mgrast_rel_2008_0919
k-class-representative_n_tree_tips.pl (dead) No revisions exist on mgrast_rel_2008_0919
k-class-tree-from-contig-dir.pl (dead) No revisions exist on mgrast_rel_2008_0919
keep_good_connections.pl (dead) No revisions exist on mgrast_rel_2008_0919
km_build_Data.pl (dead) No revisions exist on mgrast_rel_2008_0919
km_build_function_index.pl (dead) No revisions exist on mgrast_rel_2008_0919
km_build_just_otu_index.pl (dead) No revisions exist on mgrast_rel_2008_0919
km_build_kmers_part1.pl (dead) No revisions exist on mgrast_rel_2008_0919
km_build_kmers_part2.pl (dead) No revisions exist on mgrast_rel_2008_0919
km_pick_best_hit_in_peg.pl (dead) No revisions exist on mgrast_rel_2008_0919
km_process_hits_to_regions.pl (dead) No revisions exist on mgrast_rel_2008_0919
kmc (dead) No revisions exist on mgrast_rel_2008_0919
kmer_classifier.pl (dead) No revisions exist on mgrast_rel_2008_0919
kmer_guts_net.pl (dead) No revisions exist on mgrast_rel_2008_0919
kmer_property_search.pl (dead) No revisions exist on mgrast_rel_2008_0919
kmer_search.pl (dead) No revisions exist on mgrast_rel_2008_0919
kp_build_Data.pl (dead) No revisions exist on mgrast_rel_2008_0919
kp_get_properties_next_round.pl (dead) No revisions exist on mgrast_rel_2008_0919
kp_process_dna_hits.pl (dead) No revisions exist on mgrast_rel_2008_0919
kp_process_hits.pl (dead) No revisions exist on mgrast_rel_2008_0919
kp_run_tests.pl (dead) No revisions exist on mgrast_rel_2008_0919
label_all_nodes.pl (dead) No revisions exist on mgrast_rel_2008_0919
lengths_of_contigs (dead) No revisions exist on mgrast_rel_2008_0919
list_genomes (dead) No revisions exist on mgrast_rel_2008_0919
load_atomic_regulons.pl (dead) No revisions exist on mgrast_rel_2008_0919
load_chromosomal_clusters (dead) No revisions exist on mgrast_rel_2008_0919
load_ec_names (dead) No revisions exist on mgrast_rel_2008_0919
load_external_orgs (dead) No revisions exist on mgrast_rel_2008_0919
load_features (dead) No revisions exist on mgrast_rel_2008_0919
load_function_transition_table.pl (dead) No revisions exist on mgrast_rel_2008_0919
load_kegg (dead) No revisions exist on mgrast_rel_2008_0919
load_kmer_peg_db.pl (dead) No revisions exist on mgrast_rel_2008_0919
load_kmers_into_memcache.pl (dead) No revisions exist on mgrast_rel_2008_0919
load_md5_alignment.pl (dead) No revisions exist on mgrast_rel_2008_0919
load_patric_map.pl (dead) No revisions exist on mgrast_rel_2008_0919
load_pattyfams.pl (dead) No revisions exist on mgrast_rel_2008_0919
load_pch_pins (dead) No revisions exist on mgrast_rel_2008_0919
load_peg_mapping (dead) No revisions exist on mgrast_rel_2008_0919
load_propagation_locks.pl (dead) No revisions exist on mgrast_rel_2008_0919
load_protein_families (dead) No revisions exist on mgrast_rel_2008_0919
load_sets (dead) No revisions exist on mgrast_rel_2008_0919
load_sprout.pl (dead) No revisions exist on mgrast_rel_2008_0919
load_ss_classification.pl (dead) No revisions exist on mgrast_rel_2008_0919
load_wikipedia.pl (dead) No revisions exist on mgrast_rel_2008_0919
ma.cgi (dead) No revisions exist on mgrast_rel_2008_0919
ma_pipeline.pl (dead) No revisions exist on mgrast_rel_2008_0919
ma_pipeline_ecoli.pl (dead) No revisions exist on mgrast_rel_2008_0919
ma_pipeline_shewanella.pl (dead) No revisions exist on mgrast_rel_2008_0919
macapp_files_to_genome_dir.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_FIG_annotations_for_sprout.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_PATRICfams.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_PATRICfams_collapse_md5.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_PG (dead) No revisions exist on mgrast_rel_2008_0919
make_PG.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_binary (dead) No revisions exist on mgrast_rel_2008_0919
make_calls (dead) No revisions exist on mgrast_rel_2008_0919
make_coreg_conjectures_based_on_subsys.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_final_condensed_bbhs.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_indexes (dead) No revisions exist on mgrast_rel_2008_0919
make_initial_partition_scores.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_kb_md5.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_ma_html.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_md5_figfams_file.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_occ_counts (dead) No revisions exist on mgrast_rel_2008_0919
make_partition_reps.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_partition_repsW.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_predictor_input.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_predictor_input_from_gto.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_probes_to_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_proml_tree_2.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_protein_sets (dead) No revisions exist on mgrast_rel_2008_0919
make_pu_from_ids.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_pu_from_seqs.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_release.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_scored_instances.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_sim_part_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_sim_sets (dead) No revisions exist on mgrast_rel_2008_0919
make_sims_and_fc_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_sr_inconsistent_fams.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_subsys_based_families2.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_supporting_predicates.pl (dead) No revisions exist on mgrast_rel_2008_0919
make_transferable_chunks (dead) No revisions exist on mgrast_rel_2008_0919
map_pegs (dead) No revisions exist on mgrast_rel_2008_0919
mark_genome_as_phage.pl (dead) No revisions exist on mgrast_rel_2008_0919
mark_picked_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
match_to_axes.pl (dead) No revisions exist on mgrast_rel_2008_0919
match_to_genome_axes.pl (dead) No revisions exist on mgrast_rel_2008_0919
match_to_genome_frequencies.pl (dead) No revisions exist on mgrast_rel_2008_0919
merge_annotations (dead) No revisions exist on mgrast_rel_2008_0919
merge_assignments.pl (dead) No revisions exist on mgrast_rel_2008_0919
merge_gene_sets.pl (dead) No revisions exist on mgrast_rel_2008_0919
merge_missing_gene_output.pl (dead) No revisions exist on mgrast_rel_2008_0919
merge_missing_sims.pl (dead) No revisions exist on mgrast_rel_2008_0919
merge_peg_synonyms.pl (dead) No revisions exist on mgrast_rel_2008_0919
merge_translation_rules (dead) No revisions exist on mgrast_rel_2008_0919
metabolic_reconstruction.pl (dead) No revisions exist on mgrast_rel_2008_0919
modal_codon_usage.pl (dead) No revisions exist on mgrast_rel_2008_0919
modelCompare.pl (dead) No revisions exist on mgrast_rel_2008_0919
modify_tree.pl (dead) No revisions exist on mgrast_rel_2008_0919
nap.c (dead) No revisions exist on mgrast_rel_2008_0919
native_codon_usage.pl (dead) No revisions exist on mgrast_rel_2008_0919
overlap_resolution_test.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-abstract-clusters.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-aggregate-sss.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-aggregates-to-html.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-all-drugs.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-all-genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-all-subsystems.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-all-taxonomies.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-blast.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-build-kmer-db.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-closest-seqs.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-co-occur.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-collate.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-count-families.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-count.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-discriminating-kmers.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-drug-amr-data.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-echo.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-extract-gto.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-extract.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-feature-gap.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-feature-upstream.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-file-filter.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-find-couples.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-find-features.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-find-in-clusters.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-format-results.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-function-parse.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-function-to-role.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-generate-close-roles.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-generate-clusters.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-genome-amr-data.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-genome-distance.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-genome-fasta.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-genome-kmer-hits.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-genus-species.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-contig-data.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-drug-genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-family-data.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-family-features.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-feature-data.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-feature-group.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-feature-regions.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-feature-sequence.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-feature-subsystems.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-features-by-sequence.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-genome-contigs.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-genome-data.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-genome-drugs.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-genome-expression.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-genome-features.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-genome-group.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-get-genome-subsystems.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-gto-dna.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-gto-fasta.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-gto-scan.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-gto.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-head.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-identical-dna.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-identical-proteins.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-identify-clusters.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-inAandB.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-inAnotB.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-inAorB.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-join.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-kmer-compare.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-list-feature-groups.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-list-genome-groups.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-login.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-mass-cluster-run.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-match.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-merge.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-pick.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-project-subsystems.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-put-feature-group.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-put-genome-group.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-rast.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-related-by-clusters.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-rep-prots.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-role-features.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-role-matrix.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-sequence-profile.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-set-to-relation.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-signature-clusters.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-signature-families.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-signature-peginfo.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-similar-proteins-by-blast.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-similar-proteins-by-family.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-sort.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-stats.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-subsys-roles.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-tail.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-tbl-to-fasta.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-tbl-to-html.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-tests.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-uni-roles.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3-write-kmers.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3_all_features.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3_all_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3_contigs_in_genome.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-check-mcl-compute-times.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-compare-patric-calls-2.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-compare-patric-calls.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-compute-patric-update-delta.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-compute-patric-update.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-create-release-dir.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-create-split-nr-for-fams.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-eval-bin-site.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-eval-bins.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-eval-genome.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-eval-genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-eval-gto.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-eval-sort.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-propagate-family-names.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-recall-patric-proteins.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-recall-proteins.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-reduce-families-for-kser.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-setup-alignment-sync-dir.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-split-families.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-test-evaluator.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-update-propagated-family-names.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-write-family-defs.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x-write-subsystem-qa.pl (dead) No revisions exist on mgrast_rel_2008_0919
p3x_kser_parallel_load.pl (dead) No revisions exist on mgrast_rel_2008_0919
package_annotations (dead) No revisions exist on mgrast_rel_2008_0919
package_assignments (dead) No revisions exist on mgrast_rel_2008_0919
package_cleaned_bins.pl (dead) No revisions exist on mgrast_rel_2008_0919
package_code (dead) No revisions exist on mgrast_rel_2008_0919
package_fix.pl (dead) No revisions exist on mgrast_rel_2008_0919
package_lightweight_code (dead) No revisions exist on mgrast_rel_2008_0919
package_translation_rules (dead) No revisions exist on mgrast_rel_2008_0919
paint_reactions_on_tree_pipeline.pl (dead) No revisions exist on mgrast_rel_2008_0919
parse_genbank (dead) No revisions exist on mgrast_rel_2008_0919
patric_call_proteins.pl (dead) No revisions exist on mgrast_rel_2008_0919
pegs_on_contigs.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_add_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_add_role_peg.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_adjacency_of_core.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_build_fasta_for_phylogeny.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_build_newick_tree.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_build_protein_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_check_gapfills.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_compute_corr.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_compute_md5s.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_compute_subsystem_membership.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_compute_traits.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_core_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_estimate_alien_pegs.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_events.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_extract_reaction_sets.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_filter_alien.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_form_mobile_element_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_function_of.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_generate_possible_assignments.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_get_codon_usage_stats.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_get_consistency_before_after.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_get_gapfill_reactions.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_get_models.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_get_pegs_in_repeats.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_get_reaction_keys.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_get_reaction_role.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_get_reactions.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_get_stats.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_inconsistent_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_intersection.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_janaka_get_role_reactions_pegs.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_make_initial_models.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_make_md5_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_make_reaction_properties.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_make_reaction_tables.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_pipeline.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_process_pubs.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_roles_in_some_but_not_X.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_run_gapfills.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_submit_to_RAST.pl (dead) No revisions exist on mgrast_rel_2008_0919
pg_tabulate_reactions.pl (dead) No revisions exist on mgrast_rel_2008_0919
pick_feature_set.pl (dead) No revisions exist on mgrast_rel_2008_0919
place_properties_on_tree.pl (dead) No revisions exist on mgrast_rel_2008_0919
place_proteins_into_pattyfams.pl (dead) No revisions exist on mgrast_rel_2008_0919
plate_sheet_parser.pl (dead) No revisions exist on mgrast_rel_2008_0919
pop_vec.pl (dead) No revisions exist on mgrast_rel_2008_0919
possible_projections.pl (dead) No revisions exist on mgrast_rel_2008_0919
predicted_vs_actual.pl (dead) No revisions exist on mgrast_rel_2008_0919
process_evaluation.pl (dead) No revisions exist on mgrast_rel_2008_0919
process_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
process_new_sims (dead) No revisions exist on mgrast_rel_2008_0919
process_one_exp_dir.pl (dead) No revisions exist on mgrast_rel_2008_0919
process_otus.pl (dead) No revisions exist on mgrast_rel_2008_0919
project_codon_usage_onto_axis.c (dead) No revisions exist on mgrast_rel_2008_0919
pubbed_fids.pl (dead) No revisions exist on mgrast_rel_2008_0919
publish_subsystems.pl (dead) No revisions exist on mgrast_rel_2008_0919
pubseed_data_export.pl (dead) No revisions exist on mgrast_rel_2008_0919
pull_fasta_entries (dead) No revisions exist on mgrast_rel_2008_0919
put_directory_in_one_file (dead) No revisions exist on mgrast_rel_2008_0919
put_func_on_families_2c.pl (dead) No revisions exist on mgrast_rel_2008_0919
rapid_propagation2.pl (dead) No revisions exist on mgrast_rel_2008_0919
rapid_propagation3.pl (dead) No revisions exist on mgrast_rel_2008_0919
rapid_propagation4.pl (dead) No revisions exist on mgrast_rel_2008_0919
rapid_propagation5.pl (dead) No revisions exist on mgrast_rel_2008_0919
rapid_propagation_plasmid.pl (dead) No revisions exist on mgrast_rel_2008_0919
rapid_subsystem_inference_batch.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_annotate_proteins_similarity.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_build_nr_from_close_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_call_CDSs_using_prodigal.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_call_RNAs.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_call_assembly_gaps.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_call_crisprs.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_call_prophage_using_phispy.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_call_rRNAs.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_call_special_proteins.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_call_tRNAs.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_compute_specialty_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_delete_rejected_pegs.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_export_genome.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_load_specialty_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
rast_prepare_NR_directory.pl (dead) No revisions exist on mgrast_rel_2008_0919
rationalize_blast (dead) No revisions exist on mgrast_rel_2008_0919
readable_fasta.pl (dead) No revisions exist on mgrast_rel_2008_0919
rebuild_converged_Data.pl (dead) No revisions exist on mgrast_rel_2008_0919
recall_pegs.pl (dead) No revisions exist on mgrast_rel_2008_0919
recent_annotations_by_genome.pl (dead) No revisions exist on mgrast_rel_2008_0919
reduce_sims (dead) No revisions exist on mgrast_rel_2008_0919
reformat_circular_contigs.pl (dead) No revisions exist on mgrast_rel_2008_0919
reformat_dsim_dbs (dead) No revisions exist on mgrast_rel_2008_0919
reformat_sims (dead) No revisions exist on mgrast_rel_2008_0919
reindex_sim_btrees.pl (dead) No revisions exist on mgrast_rel_2008_0919
remove_multiple_occurring_probes.pl (dead) No revisions exist on mgrast_rel_2008_0919
rep_sets.pl (dead) No revisions exist on mgrast_rel_2008_0919
reps_for_wc.pl (dead) No revisions exist on mgrast_rel_2008_0919
restore_annotations (dead) No revisions exist on mgrast_rel_2008_0919
restore_assignments (dead) No revisions exist on mgrast_rel_2008_0919
restore_translation_rules (dead) No revisions exist on mgrast_rel_2008_0919
rewrite_peg_syns.pl (dead) No revisions exist on mgrast_rel_2008_0919
root_at_midpoint.pl (dead) No revisions exist on mgrast_rel_2008_0919
rs.pl (dead) No revisions exist on mgrast_rel_2008_0919
rs_create_ref_profile.pl (dead) No revisions exist on mgrast_rel_2008_0919
rs_get_intergenic_counts.pl (dead) No revisions exist on mgrast_rel_2008_0919
rs_get_peg_counts.pl (dead) No revisions exist on mgrast_rel_2008_0919
rs_get_rnas.pl (dead) No revisions exist on mgrast_rel_2008_0919
rs_pipeline.pl (dead) No revisions exist on mgrast_rel_2008_0919
run1_convergence_step.pl (dead) No revisions exist on mgrast_rel_2008_0919
run_all_fam_rel.pl (dead) No revisions exist on mgrast_rel_2008_0919
run_all_inference.pl (dead) No revisions exist on mgrast_rel_2008_0919
run_anno_to_pubseed_flow.sh (dead) No revisions exist on mgrast_rel_2008_0919
run_checkm.pl (dead) No revisions exist on mgrast_rel_2008_0919
run_coreseed_to_pubseed_flow.sh (dead) No revisions exist on mgrast_rel_2008_0919
run_gene_calling_scripts.pl (dead) No revisions exist on mgrast_rel_2008_0919
run_muscle.pl (dead) No revisions exist on mgrast_rel_2008_0919
run_rabbit_daemon.pl (dead) No revisions exist on mgrast_rel_2008_0919
run_rabbit_daemon_set.pl (dead) No revisions exist on mgrast_rel_2008_0919
run_ribo_ratio_against_pubseed.pl (dead) No revisions exist on mgrast_rel_2008_0919
salvage_on_replacement.pl (dead) No revisions exist on mgrast_rel_2008_0919
seed2ptt.pl (dead) No revisions exist on mgrast_rel_2008_0919
seed2tbl.pl (dead) No revisions exist on mgrast_rel_2008_0919
seed2txt.pl (dead) No revisions exist on mgrast_rel_2008_0919
sequence_dereplication.pl (dead) No revisions exist on mgrast_rel_2008_0919
server_paper_example1.pl (dead) No revisions exist on mgrast_rel_2008_0919
server_paper_example1a.pl (dead) No revisions exist on mgrast_rel_2008_0919
server_paper_example1b.pl (dead) No revisions exist on mgrast_rel_2008_0919
server_paper_example2.pl (dead) No revisions exist on mgrast_rel_2008_0919
server_paper_example3.pl (dead) No revisions exist on mgrast_rel_2008_0919
server_paper_example4.pl (dead) No revisions exist on mgrast_rel_2008_0919
server_paper_example5.pl (dead) No revisions exist on mgrast_rel_2008_0919
server_paper_example6.pl (dead) No revisions exist on mgrast_rel_2008_0919
server_paper_example7.pl (dead) No revisions exist on mgrast_rel_2008_0919
server_paper_figure2.pl (dead) No revisions exist on mgrast_rel_2008_0919
set-from-subtree.pl (dead) No revisions exist on mgrast_rel_2008_0919
set_by_subtree.pl (dead) No revisions exist on mgrast_rel_2008_0919
set_figfam_functions.pl (dead) No revisions exist on mgrast_rel_2008_0919
set_to_relation (dead) No revisions exist on mgrast_rel_2008_0919
sigs.pl (dead) No revisions exist on mgrast_rel_2008_0919
sims_after_adding_genome.pl (dead) No revisions exist on mgrast_rel_2008_0919
solid_rectangles_to_solid_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
sort_bbhs_by_counts.pl (dead) No revisions exist on mgrast_rel_2008_0919
sort_by_annotator.pl (dead) No revisions exist on mgrast_rel_2008_0919
sort_by_function.pl (dead) No revisions exist on mgrast_rel_2008_0919
sort_sets_of_pegs.pl (dead) No revisions exist on mgrast_rel_2008_0919
sparse_genome_sample.pl (dead) No revisions exist on mgrast_rel_2008_0919
sphinx_index_genome.pl (dead) No revisions exist on mgrast_rel_2008_0919
split_fasta.pl (dead) No revisions exist on mgrast_rel_2008_0919
split_sequences_into_sets.pl (dead) No revisions exist on mgrast_rel_2008_0919
splitup (dead) No revisions exist on mgrast_rel_2008_0919
sr_pipeline.pl (dead) No revisions exist on mgrast_rel_2008_0919
submit_corr.pl (dead) No revisions exist on mgrast_rel_2008_0919
submit_corr_to_server.pl (dead) No revisions exist on mgrast_rel_2008_0919
summarize_classification_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
summarize_genome_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
svc_fasta_to_md5.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_ACH.t (dead) No revisions exist on mgrast_rel_2008_0919
svr_CS.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_CS_pipeline.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_NCBI_sequence.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_NCBI_taxonomy.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_RNA_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_SAP.t (dead) No revisions exist on mgrast_rel_2008_0919
svr_ach_lookup.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_add_lengths_to_blast.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_add_reaction_descriptions.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_ali_to_html.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_aliases_of.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_aliases_to_pegs.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_align_seqs.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_align_using_muscle.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_aligns_with_prot.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_all_complexes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_all_experiments.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_all_features.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_all_figfams.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_all_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_all_models.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_all_reactions.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_all_roles_used_in_models.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_all_subsystems.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_assign_to_dna_using_figfams.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_assign_using_figfams.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_atomic_reg_coexp.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_atomic_regulons.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_big_repeats.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_blast.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_by_taxonomy.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_call_pegs.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_call_rnas.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_cdd_scan.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_close_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_closest_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_cluster_locations.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_cluster_pegs.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_co_occurrence.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_co_occurrence_evidence.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_cohesion_groups.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_column_of_subsystem.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_compare_feature_tables.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_complex_to_reaction.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_condense_repeats.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_contigs_in_genome.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_copy_to_RAST_dir.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_coregulated_by_correspondence.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_corr_by_exp.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_corresponding_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_corresponding_genes2.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_coupled_reactions.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_create_set.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_current_annotation.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_cut_domain.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_delete_RAST_job.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_delete_from_set.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_delete_set.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_determine_sets_of_related_contigs.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_discriminating_functions.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_distinct_otus.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_dlits.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_dna_seq.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_drug_resistance_proteins.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_enumerate_sets_by_owner.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_evidence.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_exp_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_export_as_seed_dir.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_expressed_genes_in_range.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_fasta.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_fasta_to_md5.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_fc_figfams.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_fids_for_md5.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_fids_to_ids.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_fids_to_locations.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_fids_to_regulons.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_fig_id_corr.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_figfam_fasta.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_figfam_functions.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_figfams_to_ids.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_file_to_spreadsheet.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_find_clusters_relevant_to_reaction.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_find_clusters_relevant_to_role.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_find_fused_genes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_find_hypos_for_cluster.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_find_protein.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_find_regulatory_proteins.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_function_of.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_function_to_role.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_functionally_coupled.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_gap_filled_reactions_and_roles.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_genbank_to_seed.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_genbank_to_table.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_gene_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_generate_dna_samples.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_genome_functions.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_genome_of.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_genome_statistics.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_get_ali_and_tree.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_get_all.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_get_coupling_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_get_default_dataset.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_get_rep_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_get_set.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_identical_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_ids_to_figfams.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_ids_to_subsystems.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_img_analysis.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_in_fasta.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_in_runs.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_inconsistent_sets.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_inherit_aliases.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_inherit_annotations.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_insert_seqs_into_alignment.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_intergenic_regions.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_is_hypo.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_just_ends.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_keep_only.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_kill_RAST_job.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_link_to_compare_regions.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_location_of.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_make_pan_genome_prot_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_mapped_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_mark_tree_states.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_md5_of_prot.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_members_of_otu.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_metabolic_reconstruction.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_missing_roles.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_motif.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_neighborhood_of_role.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_neighboring_reactions.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_neighbors_of.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_oligomer_similarity.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_otus.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_pegs_in_subsystems.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_pegs_with_evcode.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_possible_joins.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_preferred_roles.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_project_by_sr.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_project_model.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_protein_assertions.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_psiblast_search.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_put_set.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_quick_assign.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_rRNA.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_reaction_description.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_reaction_gain_loss_table.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_reactions_in_model.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_reactions_to_roles.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_regulons_to_fids.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_rep_seqs.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_representative_sequences.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_reroot_tree.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_retrieve_RAST_job.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_role_to_complex.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_role_to_pegs.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_roles_to_reactions.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_roles_to_subsys.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_run_RAST_jobs.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_run_rast_jobs.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_scanN.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_scanP.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_scripts.t (dead) No revisions exist on mgrast_rel_2008_0919
svr_seed_to_embl.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_seed_to_genbank.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_seed_to_table.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_sets_by_owner.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_similar_to.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_sims2html.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_sketch_tree.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_sphinx_indexing.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_split_fams.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_spreadsheet_to_file.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_ss_classes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_status_of_RAST_job.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_submit_RAST_job.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_submit_correspondences.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_subsystem_classification.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_subsystem_genome_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_subsystem_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_subsystem_roles.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_subsystem_spreadsheet.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_subsystems_to_roles.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_summarize_MG_output.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_summarize_contigs.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_summarize_protein_families.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_tab2html.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_taxonomically_related_genomes.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_taxonomy.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_tips_of_tree.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_tmpred_predictions.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_translations_of.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_tree.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_tree_to_html.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_trim_ali.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_update_assignments.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_update_corr_maps.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_upstream.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_which_genus_species.pl (dead) No revisions exist on mgrast_rel_2008_0919
svr_with_close_blast_hits.pl (dead) No revisions exist on mgrast_rel_2008_0919
tbl_to_gto.pl (dead) No revisions exist on mgrast_rel_2008_0919
tmpred_predictions.pl (dead) No revisions exist on mgrast_rel_2008_0919
to_fasta.pl (dead) No revisions exist on mgrast_rel_2008_0919
to_run_daily.sh (dead) No revisions exist on mgrast_rel_2008_0919
to_run_new_genomes.sh (dead) No revisions exist on mgrast_rel_2008_0919
tool_hdr.pl (dead) No revisions exist on mgrast_rel_2008_0919
tool_hdr_py.pl (dead) No revisions exist on mgrast_rel_2008_0919
trail.pl (dead) No revisions exist on mgrast_rel_2008_0919
translate_fasta.c (dead) No revisions exist on mgrast_rel_2008_0919
translate_fasta_6.c (dead) No revisions exist on mgrast_rel_2008_0919
uninstall (dead) No revisions exist on mgrast_rel_2008_0919
uninstall.sims (dead) No revisions exist on mgrast_rel_2008_0919
update_OTUs.pl (dead) No revisions exist on mgrast_rel_2008_0919
update_PSEED_subsystems.pl (dead) No revisions exist on mgrast_rel_2008_0919
update_SSU_rRNAs.pl (dead) No revisions exist on mgrast_rel_2008_0919
update_hope_info.pl (dead) No revisions exist on mgrast_rel_2008_0919
update_kegg_data.pl (dead) No revisions exist on mgrast_rel_2008_0919
update_phage_annotations.pl (dead) No revisions exist on mgrast_rel_2008_0919
update_sims (dead) No revisions exist on mgrast_rel_2008_0919
update_taxonomies (dead) No revisions exist on mgrast_rel_2008_0919
valid_fasta_file.pl (dead) No revisions exist on mgrast_rel_2008_0919
verify_genome_directory (dead) No revisions exist on mgrast_rel_2008_0919
verify_pegs_in_tbl (dead) No revisions exist on mgrast_rel_2008_0919
wb.pl (dead) No revisions exist on mgrast_rel_2008_0919
weak_predictors.pl (dead) No revisions exist on mgrast_rel_2008_0919
where_shifts_occurred.pl (dead) No revisions exist on mgrast_rel_2008_0919
write_go_mappings.pl (dead) No revisions exist on mgrast_rel_2008_0919

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