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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
extract_metagene_contigs.pl  1.11  11 years  arodri7   correction
load_bbhs.pl  1.15  12 years  olson  *** empty log message ***
svr_assign_to_dna_using_figfams.pl  1.6  10 years  parrello  *** empty log message ***
get_FIGfams_SS_NMPDR_stats.pl  1.1  11 years  arodri7  *** empty log message ***
seed2tbl.pl  1.2  11 years  bartels  *** empty log message ***
Consistency_Families.pm  1.1  12 years  bartels  *** empty log message ***
recompute_comparison.pl  1.1  12 years  bartels  *** empty log message ***
EmergencyMapFlipper.pl  1.2  10 years  parrello  *** empty log message ***
make_tf_equivalog_file.pl  1.1  12 years  bartels  *** empty log message ***
merge_assignments.pl  1.1  11 years  bartels  *** empty log message ***
createTIGRfamSrc.pl  1.1  12 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  12 years  wilke  *** empty log message ***
get_genomes_from_ncbi.pl  1.1  10 years  wilke  *** empty log message ***
expand_sims.pl  1.2  12 years  olson  *** empty log message ***
MFADriver.pl  1.2  11 years  chenry  *** empty log message ***
map_to_scaffold.pl  1.4  12 years  olson  Actually write out the changed entries.
build_anno_clearinghouse.pl  1.6  12 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
build_nr.pl  1.22  12 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
find_neighbors_by_sim.pl  1.4  12 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.
gd_tree.pl  1.1  11 years  golsen  Add a command line program to make a png graphic from a newick tree file.
find_selenoproteins.pl  1.4  12 years  golsen  Add functions to reference selenoproteins, and add change the set slightly. Rep...
renumber_features.pl  1.12  11 years  gdpusch  Add invocation of `formatdb` on PRG FASTA.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
gather_genome_info.pl  1.2  10 years  olson  Add more data gathering
install_features_batch.pl  1.1  12 years  olson  Add new script to install a batch of genomid.tbl / genomeid.fasta files. Initial...
svr_assign_using_figfams.pl  1.7  10 years  olson  Add support for --kmerDataset flag
align_fasta.pl  1.3  10 years  golsen  Add support for alignment with muscle.
assign_using_kmers.pl  1.8  10 years  olson  Add support for explicitly specifying FRI.db, setI.db, table.binary
index_subsystems.pl  1.11  11 years  olson  Add support for subsystem_metadata table. Updates via Subsystem::db_sync.
find_SEED_SSU_rRNA_genes.pl  1.4  11 years  golsen  Add type field to output report (always rna).
run_glimmer3.pl  1.14  10 years  parrello  Added "-verbose" option so tracing can be turned on from the servers.
to_genbank.pl  1.6  11 years  gdpusch  Added FIGV support.
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
find_missing_genes.pl  1.7  10 years  gdpusch  Added check to only accept BBHs from corresponding genes table.
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  13 years  overbeek  Added comments to expalin logic. -- gdp
add_structured_english.pl  1.4  12 years  disz  Added escape arg to structured engkish
SpanishInquisition.pl  1.1  12 years  parrello  Added for testing the Confess method.
reformat_contigs.pl  1.21  10 years  gdpusch  Added hack to split on very long homopolymer regions.
remove_embedded_pegs.pl  1.18  11 years  gdpusch  Added hooks for priority-based PEG removal; however, code does not yet appear to...
rapid_propagation_plasmid.pl  1.21  10 years  gdpusch  Added more bulletproofing, plus fallback to MGA if GLIMMER fails
WikiMaker.pl  1.6  11 years  parrello  Added more trace messages.
remove_rna_overlaps.pl  1.10  12 years  gdpusch  Added setting of VERBOSE from metafile. -- /gdp
filter_overlaps.pl  1.5  13 years  overbeek  Added some more diagnosting lines. -- /gdp
pull_orfs.pl  1.5  11 years  gdpusch  Added support for alternate genetic codes, and output of DNA rather than peptide...
run_glimmer2.pl  1.7  13 years  gdpusch  Added support for multiple genetic codes. -- /gdp
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
sequence_length_histogram.pl  1.5  10 years  olson  Additional fixes to new upload.
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.
index_sims_file.c  1.7  11 years  golsen  Bob added an #include <sys/types.h>. This is committing that code change.
index_sims.pl  1.12  11 years  olson  Bump id size.
svr_protein_assertions.pl  1.6  10 years  disz  CHanged ACHserver to SAPserver and fixed processing of return values
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.
server_paper_example2.pl  1.7  10 years  disz  Changed to use ANNO server
load_abstract_coupling.pl  1.3  14 years  parrello  Changed to use a single-character delimiter (for compatability with PostGRES).
compare_scenarios.pl  1.5  11 years  dejongh  Changes to move the 'All' scenarios directory to FIG_Config::global/Models/All
analyze_scenario_connections.pl  1.4  11 years  dejongh  Changes to move the 'All' scenarios directory to FIG_Config::global/Models/All
valid_fasta_file.pl  1.1  10 years  olson  Check to ensure a fasta file is valid.
diff_tbls.pl  1.1  14 years  overbeek  Computes difference betwween two tbl files. -- /gdp
insert_prot_into_tree.pl  1.14  13 years  golsen  Continuing the update of tree packages and programs
convert-blast-to-m8.pl  1.1  11 years  olson  Convert full blast output to -m8 output using Gary's blast parsing code.
TestLocations.pl  1.8  12 years  parrello  Converted to use new name for Contrain method.
server_paper_example7.pl  1.4  10 years  chenry  Corrected a few bugs in the example script.
ModelDriver.pl  1.14  10 years  chenry  Created server paper example. Made minor changes to model driver. Corrected a bu...
find_protein_homologs.pl  1.1  12 years  golsen  Debugging and adding support of all the NCBI genetic codes.
server_paper_example1.pl  1.12  10 years  parrello  Documentation fix for server paper.
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.
fastasize.c  1.3  14 years  olson  Doh, put proper comments in for C code.
renumber_seed_dir.pl  1.4  10 years  olson  Don't fail if Features dir does not exist.
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  13 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  13 years  hwang  Files to get journal information from PubMed
form_clusters.pl  1.2  10 years  parrello  Final Server updates.
promote_orfs_to_pegs.pl  1.13  12 years  gdpusch  Final clean-up. -- /gdp
svr_delete_RAST_job.pl  1.3  10 years  olson  Fix 666666 problem. Add support for using the test server.
make_indexes.pl  1.17  10 years  dejongh  Fix KEGG location
load_kegg.pl  1.15  10 years  dejongh  Fix KEGG location
compute_genome_counts.pl  1.25  11 years  olson  Fix bug where compute_genome_counts fails to run on a genome directory with mult...
FFB2_get_oligos.pl  1.2  10 years  olson  Fix bug with overloaded hashes.
compute_translation_MD5.c  1.2  10 years  olson  Fix index_translation and add_assertions_of_function issues.
index_translations.pl  1.23  10 years  olson  Fix index_translation and add_assertions_of_function issues.
index_translation_files.c  1.7  10 years  olson  Fix index_translation and add_assertions_of_function issues.
add_assertions_of_function.pl  1.37  10 years  olson  Fix index_translation and add_assertions_of_function issues.
find_gaps.pl  1.9  11 years  gdpusch  Fixed (hopefully) incorrectly handled out-of-bounds cases.
svr_similar_to.pl  1.2  10 years  parrello  Fixed POD errors.
svr_aliases_of.pl  1.4  10 years  parrello  Fixed POD errors.
svr_all_features.pl  1.5  10 years  parrello  Fixed POD errors.
svr_ids_to_subsystems.pl  1.4  10 years  parrello  Fixed POD errors. Added examples.
svr_all_subsystems.pl  1.9  10 years  parrello  Fixed POD errors. Added examples.
svr_gene_data.pl  1.2  10 years  parrello  Fixed POD errors. Added examples.
svr_pegs_in_subsystems.pl  1.5  10 years  parrello  Fixed POD errors. Added examples.
svr_ach_lookup.pl  1.9  10 years  parrello  Fixed POD errors. Added examples.
svr_fasta.pl  1.10  10 years  parrello  Fixed POD errors. Added examples.
svr_in_runs.pl  1.5  10 years  parrello  Fixed POD errors. Added examples.
svr_neighbors_of.pl  1.3  10 years  parrello  Fixed POD errors. Added examples.
svr_ids_to_figfams.pl  1.5  10 years  parrello  Fixed POD errors. Added examples.
svr_figfam_fasta.pl  1.3  10 years  parrello  Fixed POD errors. Added examples.
svr_upstream.pl  1.7  10 years  parrello  Fixed POD errors. Added examples.
exclude_genomes.pl  1.3  12 years  parrello  Fixed a POD error.
import_similarity_bundle.pl  1.3  12 years  parrello  Fixed a POD error.
backup_subsystems.pl  1.3  12 years  parrello  Fixed a POD error.
find_genes_based_on_kmers.pl  1.3  10 years  gdpusch  Fixed bug handling keep_genecalls.
feature_length_histogram.pl  1.3  12 years  gdpusch  Fixed duplicated ID bug, plus minor cosmetic changes. -- /gdp
parse_genbank.pl  1.28  10 years  gdpusch  Fixed fact that we are still handling RNA functions as aliases, not functions.
server_paper_example6.pl  1.3  10 years  parrello  Fixed for server paper.
make_genome_dir_for_close.pl  1.9  12 years  gdpusch  Fixed handling of spliced loci. -- /gdp
assess_completeness.pl  1.9  11 years  gdpusch  Fixed leading-whitspace bug.
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.
update_OTUs.pl  1.3  10 years  gdpusch  Fixed pattern to recognize several variations on "16S ribosomal RNA."
extract_DNA_for_whole_ORFs.pl  1.4  11 years  gdpusch  Fixed possible DNA case sensitivity.
find_neighbors.pl  1.38  10 years  gdpusch  Fixed problem finding Universals.
trace.pl  1.3  12 years  parrello  Fixed so that the destination is not case-sensitive.
server_paper_example4.pl  1.3  10 years  parrello  Fixed to use the correct servers.
svr_translations_of.pl  1.4  10 years  parrello  Fixed to work with no input.
svr_update_assignments.pl  1.3  10 years  gdpusch  Fixed typo.
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...
write_go_mappings.pl  1.1  10 years  olson  Given a genome directory, emit a table mapping id to function & go terms.
load_sims.pl  1.10  14 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  12 years  olson  Index scripts for FIGV accleration.
index_figv_annos.pl  1.1  12 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  12 years  olson  Introduct &FIG::get_figfams_data()
check_figfams.pl  1.6  12 years  olson  Introduct &FIG::get_figfams_data()
test_figfam_placement_into_families.pl  1.9  12 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. ...
macapp_files_to_genome_dir.pl  1.1  10 years  olson  MacRast support.
build_figfam_pssm_db.pl  1.2  13 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
alignment_to_html.pl  1.2  10 years  golsen  Minor updates.
svr_determine_sets_of_related_contigs.pl  1.3  10 years  olson  Misc server fixes
svr_retrieve_RAST_job.pl  1.3  10 years  olson  Misc server fixes
test_figfam_FF_peg.pl  1.3  12 years  olson  Missed one of the figfamdata fixes.
remove_clustered_pchs2.pl  1.1  13 years  olson  Missing scripts.
remove_sims_not_in_nr.pl  1.1  13 years  olson  Missing scripts.
maint-remove-obsolete-aliases.pl  1.1  13 years  olson  Missing scripts.
remove_clustered_pchs3.pl  1.1  13 years  olson  Missing scripts.
compute_genome_similarity.pl  1.1  13 years  olson  Missing scripts.
register_genome_with_clearinghouse.pl  1.1  13 years  olson  Missing scripts.
index-pegsyn.pl  1.1  13 years  olson  Missing scripts.
check_fasta_for_dups.pl  1.1  13 years  olson  Missing scripts.
representative_sequences.pl  1.4  13 years  golsen  Modifications to control ordering of sequences in representative sets and in seq...
backfill_gaps.pl  1.19  11 years  gdpusch  Modified to allow "close_genome_file" entries to be OrgDirs.
build_initial_objects_for_start_predictions.pl  1.12  12 years  gdpusch  Modified to also work on new genomes using "FIGV.". -- /gdp
get_fasta_for_tbl_entries.pl  1.11  10 years  gdpusch  Modified to remove complaints about uninitialed values when TBL entry does not c...
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...
fig_rpc.pl  1.4  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  13 years  golsen  Moving some tree building tools into packages.
add_prots_to_tree.pl  1.1  13 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.
get_pairs.pl  1.1  11 years  parrello  New script to find certain functional roles close together.
pubbed_fids.pl  1.1  10 years  parrello  New script to find features with publications attached.
svr_all_figfams.pl  1.1  10 years  parrello  New script to list all features in figfams.
Tracer.pl  1.1  11 years  parrello  New script used to route STDERR messages to the trace log.
make_overlap_report.pl  1.20  12 years  gdpusch  No longer complains about split loci. -- /gdp
rep_sets.pl  1.1  10 years  disz  Old code finally checked in to create representative sets
load_links.pl  1.7  11 years  olson  Only load links from files ending in "links" (rather than files with it anywhere...
explore_subsys_pmid.pl  1.5  13 years  hwang  PEG information is no longer stored in the file. Parsing of the file in this scr...
extract_fasta_idmap.pl  1.1  14 years  overbeek  RAE: Adding FigKernelScripts/extract_fasta_idmap.pl
nmpdr2gff.pl  1.1  14 years  overbeek  RAE: Changes to gff3 files for NMPDR and adding nmpdr2gff for creating the files...
read_write_excel.pl  1.1  14 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  14 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  14 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  14 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  14 years  olson  Remove debugging.
server_paper_figure2.pl  1.2  10 years  parrello  Removed genetic codes so program fits better on a page.
LigandCleanup.pl  1.2  12 years  parrello  Removed obsolete use clases.
TransactFeatures.pl  1.20  12 years  parrello  Removed obsolete use clause.
NMPDRAnalysis.pl  1.5  12 years  parrello  Removed obsolete use clauses.
OneShotAttributeAdder.pl  1.2  12 years  parrello  Removed obsolete use clauses.
purge_fasta.pl  1.1  14 years  overbeek  Removes duplicate entries from fasta file. -- /gdp
purge_tbl.pl  1.1  14 years  overbeek  Removes duplicate entries from tbl file. -- /gdp
make_proml_tree.pl  1.6  13 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
make_proml_tree_0.pl  1.1  13 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
verify_genome_directory.pl  1.39  11 years  gdpusch  Replaced all instances of `cat $file` and `head -1 $file` with &FIG::file_read($...
call_genome_using_glimmer.pl  1.3  11 years  gdpusch  Rewrite to remove overlap removal.
gff2tab.pl  1.5  13 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
compute_pchs_from_sims.pl  1.2  13 years  olson  Rollup of changes for the new RAST install.
build_nr_sources.pl  1.14  13 years  olson  Rollup of various rast-related changes.
process_new_sims.pl  1.6  13 years  olson  Rollup of various rast-related changes.
show_structured_english.pl  1.1  12 years  disz  Ross's code to generate annotations for NCBI
svr_function_of.pl  1.4  10 years  disz  SAS component
map-nr-ids-to-ncbi-std.pl  1.1  12 years  olson  Script to map IDs in a SEED NR into forms acceptable to the indexed NCBI fasta p...
load_peg_mapping.pl  1.11  11 years  golsen  Some code clean-up and optimization. Pretty moot since all of the time is in th...
assess_gene_call_quality.pl  1.12  11 years  gdpusch  Stuck in a plasmid hack, until we figure out how to handle plasmids properly.
build_sas_distro.pl  1.6  10 years  olson  Support building SAS distribution from clean CVS export.
build_sas_distro_from_cvs.pl  1.1  10 years  olson  Support building SAS distribution from clean CVS export.
Makefile.cprogs  1.2  12 years  olson  Support compilation of nap.c
find_special_proteins.pl  1.4  11 years  gdpusch  Suppress writing "called_by" and "special_pegs" when "-keep" is selected. -- /gd...
find_genes_based_on_neighbors.pl  1.24  10 years  olson  Switch to FFs and FF instead of FigFams and FigFam
find_neighbors_using_figfams.pl  1.11  10 years  olson  Switch to FFs and FF instead of FigFams and FigFam
find_genes_in_families.pl  1.22  10 years  olson  Switch to FFs and FF instead of FigFams and FigFam
blastP.pl  1.1  10 years  olson  Switch to using assign_functions_to_prot_set in assign_using_kmers.pl. Add blast...
FIGMODELscheduler.pl  1.3  10 years  chenry  Switched over the PPO as the system for holding the job queue tables.
server_paper_example5.pl  1.3  10 years  disz  Switched to ANNO server
PickGeneBoundariesTest.pl  1.1  12 years  parrello  Test script for backfill.
to_arabidopsis.pl  1.1  13 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
check_all_subsystems.pl  1.11  11 years  olson  Transform the single big select into a prepared statement on per-role select.s
align_with_clustal_2.pl  1.4  13 years  golsen  Trivial format change.
bielefeld_tarfile_to_seed.pl  1.7  13 years  overbeek  Tweaked usage msg. -- /gdp
update-caches.pl  1.1  13 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.
add_to_alignment.pl  1.7  11 years  golsen  Use faster version of add_to_alignment.
make_fasta_btree.pl  1.1  12 years  olson  Utility for creating btree access for fasta files.
load_wikipedia.pl  1.1  10 years  olson  Wikipedia cache loader.
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
svr_fig_id_corr.pl  1.4  10 years  overbeek  add -precise option
generate_GO_attributes.pl  1.1  13 years  overbeek  add GO attribute genertation
svr_align_using_muscle.pl  1.1  10 years  overbeek  add SAS component
svr_rep_seqs.pl  1.2  10 years  overbeek  add SAS component
correct_frameshifts.pl  1.19  10 years  overbeek  add a line describing template
sketch_tree.pl  1.2  13 years  overbeek  add ability to insert sequences into a tree
fabric_vec.pl  1.1  11 years  overbeek  add ability to make fabric vecs
add_to_subsystems.pl  1.1  13 years  overbeek  add add_to_subsystems
best_tree_using_proml_on_cluster.pl  1.1  13 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
make_sim_part_data.pl  1.1  11 years  overbeek  add command to build similarity partitions
runclustalw.pl  1.4  13 years  overbeek  add computation of alignments to building FIGFAMS
filter_figfams.pl  1.2  13 years  overbeek  add computation of alignments to building FIGFAMS
figfam.pl  1.22  12 years  overbeek  add connections between FIGfams and structures
ff.pl  1.6  12 years  overbeek  add connections between FIGfams and structures
fig.pl  1.152  10 years  overbeek  add coupled_to_batch
fasta_size.pl  1.1  11 years  overbeek  add fasta_size
find_poss_errs.pl  1.1  11 years  overbeek  add find_poss_errs and fix documentation in fig.pl
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  13 years  overbeek  add last round of phylogeny tools
COPYING.TXT  1.1  14 years  olson  add license file
reps_and_close.pl  1.2  13 years  overbeek  add make_trimmed_alignment_from_ids
FFB2_update_FIGfams.pl  1.3  10 years  olson  add missing use
new_versions_of_features.pl  1.1  14 years  overbeek  add new_versions_of_features
install_new_coupling_data.pl  1.3  12 years  olson  add option to install from a jobdir
assign_figfam.pl  1.1  11 years  arodri7  add original assign_using_ff
potentially_missed_assignments.pl  1.1  13 years  overbeek  add potentially_missed_assignments
make_parallel_proml_run.pl  1.2  13 years  overbeek  add rates to phylogeny stuff
to_structured_english.pl  1.1  12 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
ma_pipeline_shewanella.pl  1.5  10 years  overbeek  add splitting clusters
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  12 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
svr_status_of_RAST_job.pl  1.4  10 years  olson  add url argument
align_seqs.pl  1.1  13 years  overbeek  add utilities for computing alignments
order_seqs_on_length.pl  1.1  13 years  overbeek  add utilities for computing alignments
compute_sim_chunk.pl  1.3  14 years  olson  add working-on-chunk support
make_sims_and_fc_data.pl  1.1  11 years  overbeek  add wrapper to building partition-based similarity and fc data
install_partitions.pl  1.4  11 years  arodri7  added changes to update procedure
update_hope_info.pl  1.4  10 years  dejongh  added comments
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_reload_contrib.pl  1.2  11 years  wilke  added db handle in ach call
ma.cgi  1.1  10 years  overbeek  added massaging and voting
aclh.pl  1.11  12 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
reformat_circular_contigs.pl  1.1  11 years  arodri7  added reformat_circular_contigs for rapid_propagation_plasmids
meta.pl  1.12  10 years  jared  added update_path
blastp_pseq.pl  1.6  10 years  redwards  adding a default cutoff
blast2gff.pl  1.22  11 years  redwards  adding an annotation evidence that notes where calls come from
load_ss_classification.pl  1.1  11 years  redwards  adding ss classification methods
dump_ss_classification.pl  1.1  11 years  redwards  adding ss classification methods
make_initial_partition_scores.pl  1.1  11 years  overbeek  additions to support partitioning of sims
find_subsys.pl  1.3  12 years  overbeek  allow loose matching in rapid_propagation
predicted_vs_actual.pl  1.1  11 years  overbeek  basic metagenomic tools
compareMR.pl  1.1  13 years  overbeek  basic stuff for comparing metabolic reconstructions
blast_pdb_against_nr_on_tla.pl  1.1  13 years  mkubal  blast pdb against nr
index_annotations.pl  1.11  12 years  olson  bugfix
salvage_annotations.pl  1.6  14 years  olson  bugfix.
make_uniprot_corr.pl  1.2  12 years  overbeek  build uniprot correspondence
compute_PCA_with_metagenomes_as_variables.pl  1.1  11 years  mkubal  called by PCA_mgav
compute_PCA_for_metagenomes.pl  1.1  11 years  mkubal  called by PCA_ssav
exec-cgi.pl  1.1  10 years  olson  cgi executor for mac rast
subsys2pubmed.pl  1.4  13 years  hwang  change script to add new attribute after each subsystem versus after all subsyst...
make_SignalP_attributes.pl  1.2  13 years  mkubal  changed ; to :: for key separator
make_CELLO_and_TMPRED_attributes.pl  1.2  13 years  mkubal  changed ; to :: for key separator
make_ncbi_files.pl  1.4  13 years  wilke  changed check for existing directories
make_sp_uni_files.pl  1.4  13 years  wilke  changed check for input and output directory the directories may exists, so don'...
identify_organism.pl  1.2  10 years  olson  changes for new server stuff
extract_genomes.pl  1.38  14 years  overbeek  changes to support dynamic sims and updates
adjacent.pl  1.3  12 years  redwards  changing chop to chomp
pegs_in_subsystem.pl  1.6  11 years  overbeek  check for aux roles
partition_prots.pl  1.4  11 years  overbeek  check to make sure sims are working
prepare_metagenome_files_for_ftp.pl  1.3  12 years  mkubal  checks for PUBLIC file
pick_feature_set.pl  1.1  11 years  overbeek  choose genes from candidates
difference_between_two_databases.pl  1.1  11 years  redwards  code for generating the delta between two databases
estimated_fabric.pl  1.1  11 years  overbeek  code for processing fabrics and population estimates
pop_vec.pl  1.1  11 years  overbeek  code for processing fabrics and population estimates
ma_pipeline.pl  1.1  10 years  overbeek  code from Hope
SplitGeneSets.R  1.1  10 years  overbeek  code from Hope
Pipeline.R  1.1  10 years  overbeek  code from Hope
merge_gene_sets.pl  1.1  10 years  overbeek  code from Hope
ShewanellaRMA.R  1.1  10 years  overbeek  code from Hope
compute_pc.pl  1.1  10 years  overbeek  code from Hope
make_probes_to_genes.pl  1.1  10 years  overbeek  code from Hope
generate_ilits.pl  1.2  12 years  overbeek  code relating to dlit/ilit maintenance
generate_ilit_ev_codes.pl  1.4  12 years  overbeek  code relating to dlit/ilit maintenance
flatten_attribute_files.pl  1.1  10 years  redwards  code to reduce the complexity of transaction_log files
install_partition_reps.pl  1.2  10 years  arodri7  commit change
make_partition_reps_worker.pl  1.3  10 years  arodri7  commit change
generate_partitions_worker.pl  1.3  10 years  arodri7  commit change
generate_partitionsP.pl  1.5  10 years  arodri7  commit change
make_partition_repsP.pl  1.4  10 years  arodri7  commit change
make_subsys_based_families2.pl  1.1  10 years  arodri7  commit changes
propagate_subsys_changes_to_figfams.pl  1.12  10 years  arodri7  commit changes
figfam_quality_control.pl  1.8  10 years  arodri7  commit changes
compare_figfam_release_results.pl  1.5  10 years  arodri7  commit changes
figfam_subsystems.pl  1.2  10 years  arodri7  commit changes
assign_using_ff.pl  1.9  10 years  arodri7  commit changes
cleanup_figfams_updates.pl  1.1  10 years  arodri7  commit changes
submit_ff_test.pl  1.6  10 years  arodri7  commit changes
update_FIGfams.pl  1.12  10 years  arodri7  commit changes
index_nr.pl  1.2  13 years  olson  compute length btree also
make_sim_tab.pl  1.8  13 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
server_paper_example3.pl  1.5  10 years  disz  converted to new SAP server
Makefile  1.22  10 years  overbeek  copy R scripts too
genbank2fasta.pl  1.2  10 years  redwards  correcting ORIGIN regexp
correct_gff_missing_contigs.pl  1.5  12 years  redwards  correcting a weird error
check_consistency_of_sample.pl  1.7  10 years  redwards  correcting looping through parts of the genomes
bring_tree_up_to_ali.pl  1.5  13 years  overbeek  debugged version of bring_tree_up_to_ali
make_neigh_joining_tree.pl  1.8  13 years  overbeek  debugged version of bring_tree_up_to_ali
evaluate_quality_of_trees.pl  1.4  13 years  overbeek  debugged version of bring_tree_up_to_ali
uni_lit_to_dlits.pl  1.1  12 years  overbeek  dlit support
pull_fasta_entries.pl  1.8  11 years  olson  do not attempt to remap incoming ids
compute_ev_code_attributes.pl  1.2  12 years  overbeek  do not include cluster-based subsystems in forming evidence codes
make_subsys_based_families.pl  1.14  11 years  overbeek  do not use genomes with variants beginning with an asterisk in forming FIGfams b...
update_lineage.pl  1.3  12 years  wilke  draft version to update FIG taxonomy entries
dp.pl  1.4  10 years  redwards  editing header info
make_figfams.pl  1.3  13 years  overbeek  families.2c should get current function - not family function
fast_blastp.pl  1.1  12 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
build_prok_nonff_fasta.pl  1.2  10 years  olson  figfam build updates
FFB2_run_tests.pl  1.1  10 years  olson  figfam build updates
FFB2_compare_tests.pl  1.1  10 years  olson  figfam build updates
FFB2_build_updated_FF.pl  1.5  10 years  olson  figfam build updates
find_approx_neigh.pl  1.1  10 years  overbeek  find neighbors based on assigned functions and blast
sequence_dereplication.pl  1.1  11 years  arodri7  first version of sequence_dereplication. Script takes sequences which are subset...
svr_copy_to_RAST_dir.pl  1.3  10 years  olson  fix
extract_sp_links.pl  1.3  13 years  olson  fix -h error
find_rnas.pl  1.2  10 years  olson  fix ANNOserver args
call_genes.pl  1.4  10 years  olson  fix ANNOserver args
initialize_figfams.pl  1.11  10 years  overbeek  fix MySQL timeouts
backup_critical_data.pl  1.5  11 years  olson  fix bug that kept subsystems from being backedup
make_peg_map_from_tbl.pl  1.3  11 years  olson  fix bug that made empty output
myjoin.pl  1.1  14 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
pegs_in_subsystems.pl  1.8  10 years  overbeek  fix documentation
run_gene_calling_scripts.pl  1.3  11 years  overbeek  fix first arg on call to mark_picked_genes
reduce_sims.pl  1.12  11 years  olson  fix nasty little bug that drops sims
mark_picked_genes.pl  1.2  11 years  overbeek  fix order of arguments
split_and_trim_sequences.pl  1.14  13 years  overbeek  fix problem when repeats occur
rapid_propagation2.pl  1.4  10 years  olson  fix problem with new format of found file
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  12 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  13 years  mkubal  fix to score format
make_CDD_attributes.pl  1.2  13 years  mkubal  fix to score format
make_IPR_PFAM_GO_attributes.pl  1.3  13 years  mkubal  fix to score format
make_PROSITE_PIR_PRODOM_attributes.pl  1.3  13 years  mkubal  fix to score format
index_contig_files.c  1.5  14 years  olson  fix to work on 64-bit linux
call_coregulated_clusters_on_chromosome.pl  1.5  10 years  overbeek  fix typo
init_FIG.pl  1.12  10 years  olson  fix typo
to_prodom.pl  1.7  10 years  olson  fix updated URL
svr_kill_RAST_job.pl  1.4  10 years  olson  fix usage message
cache_comparison_data.pl  1.11  11 years  paczian  fixed load order of function files in RAST vs SEED organisms
find_miscalled_genes.pl  1.3  10 years  gdpusch  fixed missing declaration
create_ff_covering_skeleton.pl  1.2  11 years  arodri7  fixed script that creates a directory structure for a FIGfam for its sequence co...
trim_sequences.pl  1.11  10 years  overbeek  fixes bug in handling multidomain prots
get_neighbors_and_corr_to_ref.pl  1.6  10 years  olson  fixes for distribution
split_clean_unclean_families.pl  1.4  14 years  overbeek  fixes for splitting families into clean/unclean
export_ACH_resolution_DB.pl  1.2  12 years  overbeek  fixes relating to comments
assign_to_close_strains.pl  1.10  14 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...
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
connections_between.pl  1.8  11 years  overbeek  fixes to making close strain data
make_close_strain_data.pl  1.14  11 years  overbeek  fixes to making close strain data
load_ACH_resolution_DB.pl  1.4  12 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
make_close_strain_family_tabs.pl  1.2  14 years  overbeek  fixes to wseekly statistics
find_bad_conflicts.pl  1.1  14 years  overbeek  fixes to wseekly statistics
make_proposed_assignments_for_consistency.pl  1.4  14 years  overbeek  fixes to wseekly statistics
seed2genbank.pl  1.5  10 years  redwards  fixing major bug that was removing all stop positions
run_remote_Phobius_for_genome.pl  1.1  12 years  mkubal  for single genome
test_Observation.pl  1.1  13 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  12 years  mkubal  full loop
mg_user_id_to_unique.pl  1.2  12 years  mkubal  full loop
cluster_objects.pl  1.3  12 years  overbeek  generalize cluster_objects
ensure_genome_registration.pl  1.1  13 years  olson  generate feature registration stuff
build_all_prok_seqs.pl  1.1  10 years  overbeek  get all protein sequences for complete prokaryotic genomes
get_taxid_journals.pl  1.1  13 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_rna_features_for_calling_genes.pl  1.2  11 years  overbeek  get rid of proteins
conditionally_assign.pl  1.5  11 years  overbeek  get rid of warning and update conditionally_assign
get_NCBI_genome_attributes.pl  1.1  12 years  arodri7  get_NCBI_genome_attributes searches the NCBI internet sites for genome attribute...
get_translations.pl  1.3  14 years  overbeek  get_translations can take PEG ids from STDIN
seed2gff.pl  1.36  12 years  redwards  getting rid of need for strain info
split_sequences_into_sets.pl  1.5  10 years  overbeek  handle asym connections
same_figfam.pl  1.2  12 years  overbeek  handle bad input in same_figfam
metagenome2genbank.pl  1.4  12 years  mkubal  includes data from meta.xml
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  13 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  13 years  redwards  just a simple attribute loader
score_dfcs_mcauliffe.pl  1.5  13 years  overbeek  limit decimal positions in score
update_nr_cycle.pl  1.6  14 years  overbeek  load ext org table on update_nr_cycle
build_new_figfam_release.pl  1.4  12 years  arodri7  made default procedure the ross hack for new families
assign_using_ff_parallel.pl  1.2  11 years  arodri7  made updates to functions used for updating FIGfams
clustered_hypotheticals.pl  1.2  10 years  overbeek  major rewrite
WebAppBackend.pl  1.2  11 years  jared  make user and org commands case insensitive
pubmed_gene2peg.pl  1.2  13 years  redwards  making sure gene id is right
make_scored_instances.pl  1.4  11 years  overbeek  minor changes
run_muscle.pl  1.2  11 years  overbeek  minor fix
svr_tab2html.pl  1.3  10 years  overbeek  minor fix
check_subs_and_split_warnings.pl  1.3  12 years  overbeek  minor fix to handle deleted subsystems
make_peg_maps.pl  1.3  14 years  overbeek  minor fixes
make_coreg_conjectures_based_on_subsys.pl  1.2  10 years  overbeek  minor fixes
svr_corresponding_genes.pl  1.20  10 years  overbeek  minor fixes
trim_alignment.pl  1.2  13 years  overbeek  minor fixes
export_similarity_request.pl  1.3  14 years  overbeek  minor fixes to assignment for close strains
curator_of.pl  1.1  14 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  14 years  overbeek  minor tools
compute_changed_ids_for_nrs.pl  1.5  11 years  olson  misc fixes
update_sims2.pl  1.5  11 years  olson  misc updates
glue_tbl_to_metabolic_reconstruction.pl  1.1  10 years  olson  more anno server fixes, add some missing files
assign_to_dna_using_kmers.pl  1.5  10 years  olson  more anno server fixes, add some missing files
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...
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
make_peg_maps_from_fasta.pl  1.2  11 years  olson  need to compute sims both directions because connections_between now uses bbhs.
index_pins.pl  1.3  14 years  olson  new pin indexer
make_reduce_sims_index.pl  1.1  12 years  olson  new script
analyze_kmer_assignments.pl  1.1  10 years  olson  new script to compare output of assign_using_kmers to current SEED assignments
FFB2_usable_motifs.pl  1.1  10 years  overbeek  new scripts for updating FIGfams and Kmer tables
FFB2_merge_oligos.pl  1.1  10 years  overbeek  new scripts for updating FIGfams and Kmer tables
FFB2_load_oligo_index.pl  1.1  10 years  overbeek  new scripts for updating FIGfams and Kmer tables
FFB2_make_subsys_based_families.pl  1.1  10 years  overbeek  new scripts for updating FIGfams and Kmer tables
FFB2_create_binary_kmers.pl  1.1  10 years  overbeek  new scripts for updating FIGfams and Kmer tables
FFB2_get_prot_gs_oligos.pl  1.1  10 years  overbeek  new scripts for updating FIGfams and Kmer tables
svr_ACH.t  1.1  10 years  olson  new tests
index-pegsyn2.pl  1.1  12 years  olson  new version of pegsyn indexer that presorts data before inserting into the btree...
split_assignments_based_on_subsystems.pl  1.1  14 years  overbeek  next version of the STAG code
svr_run_RAST_jobs.pl  1.5  10 years  olson  nonActive mods
svr_submit_RAST_job.pl  1.11  10 years  olson  nonActive mods
compute_mw_and_pi.pl  1.2  13 years  mkubal  one genome at a time
get_ss_connections.pl  1.12  10 years  redwards  only call if not in a ss
make_FigFamsData.pl  1.4  14 years  overbeek  order generated FIGfams
order_figfams.pl  1.1  14 years  overbeek  order_figfams
assign_using_ff_original.pl  1.1  11 years  arodri7  original format of assign_using_ff
find_genes_based_on_neighbors_par.pl  1.1  10 years  olson  parallel version of find_genes_based_on_neighbors
EcoliRMA.R  1.1  10 years  overbeek  pipeline for Ecoli
ma_pipeline_ecoli.pl  1.2  10 years  overbeek  pipeline for Ecoli
check_for_new_genomes.pl  1.3  11 years  overbeek  print stats as you go
make_interpro_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
make_Ontology_database.pl  1.3  12 years  mkubal  provides usage when no argument given
make_go_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
make_prosite_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
make_cdd_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
make_pir_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
make_pdb_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
make_pfam_ontology.pl  1.4  12 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
sims_all.pl  1.6  11 years  overbeek  remove paralogs before computing conections
svr_metabolic_reconstruction.pl  1.2  10 years  olson  remove redundant metabolic_reconstruction.pl, update svr_metabolic_reconstructio...
update_kegg_data.pl  1.6  10 years  dejongh  removed comment
gff2seed.pl  1.29  11 years  redwards  removing check for refseq ids
summarize_taxonomy_by_blast.pl  1.9  12 years  redwards  removing fatal error if 0 or 1 hits
build_partition_index.pl  1.1  12 years  overbeek  return empty list of failure to open FIFfam
make_trimmed_alignment_from_ids.pl  1.13  12 years  overbeek  return empty list of failure to open FIFfam
rapid_subsystem_inference.pl  1.15  11 years  olson  revert changes
index_translations_MD5.pl  1.4  11 years  olson  revert changes
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.
compute_contig_md5.pl  1.4  13 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  13 years  mkubal  run iprscan on cluster
run_remote_PHOBIOUS.pl  1.1  12 years  mkubal  runs Phobius computation for given geneome
make_md5_figfams_file.pl  1.1  11 years  arodri7  script makes the md5 to figfams file
svr_column_of_subsystem.pl  1.1  10 years  olson  server script to pull a subsystem colum
update_taxonomies.pl  1.8  13 years  overbeek  set longer gap between accessing NCBI
filter_tbl_overlaps.pl  1.10  14 years  overbeek  set up find_neighbors to handle existing genomes
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  13 years  overbeek  strip comments on functions for subsystem checking
compare_two_sets_of_calls.pl  1.3  11 years  overbeek  stuff for gene calling
generate_comparisons.pl  1.1  11 years  overbeek  stuff for gene calling
generate_picked.pl  1.1  11 years  overbeek  stuff for gene calling
subsys_info.pl  1.1  12 years  overbeek  subsys_info is subsystem information for Verionika
load_ec_names.pl  1.6  11 years  olson  support for change in format to the KEGG/ECtable.
check_model_v2.pl  1.2  11 years  dejongh  switch to scenario_directory
make_model_spreadsheets.pl  1.2  11 years  dejongh  switch to scenario_directory
run_flux_optimization.pl  1.4  11 years  dejongh  switch to scenario_directory
find_missing_lib_inputs.pl  1.6  11 years  dejongh  switch to scenario_directory
find_missing_lib_inputs_v2.pl  1.2  11 years  dejongh  switch to scenario_directory
run_model_generation.pl  1.17  11 years  dejongh  switch to scenario_directory
find_essential_reactions.pl  1.3  11 years  dejongh  switch to scenario_directory
make_SBML_model.pl  1.6  11 years  dejongh  switch to scenario_directory
find_model_information.pl  1.7  11 years  dejongh  switch to scenario_directory
check_for_scenario_reachability.pl  1.3  11 years  dejongh  switch to scenario_directory
find_model_cofactors.pl  1.7  11 years  dejongh  switch to scenario_directory
make_MFA_tool_input.pl  1.2  11 years  dejongh  switch to scenario_directory
make_MPS_model.pl  1.7  11 years  dejongh  switch to scenario_directory
find_model_information_v2.pl  1.2  11 years  dejongh  switch to scenario_directory
run_scenarios.pl  1.5  11 years  dejongh  switch to scenario_directory
make_MPS_model_v2.pl  1.2  11 years  dejongh  switch to scenario_directory
run_model_generation_v3.pl  1.3  11 years  dejongh  switch to scenario_directory
check_model.pl  1.7  11 years  dejongh  switch to scenario_directory
generate_dlit_ev_codes.pl  1.5  12 years  overbeek  switching to new ilidt/dlit stuff
compute_CELLO_and_TMPRED.pl  1.2  13 years  mkubal  test for dir exist
submit_genome_to_signalP.pl  1.2  13 years  mkubal  test for dir exist
submit_genome_to_rpsblast_against_CDD_on_biocluster.pl  1.2  13 years  mkubal  test for dir exist
get_journals_for_org.pl  1.1  13 years  hwang  this script is the backend to get journals using taxonomy id or name. This calls...
load_close.pl  1.9  13 years  overbeek  tighten length constraints for figfam matching
direct_functional_coupling.pl  1.4  13 years  overbeek  tighten length constraints for figfam matching
make_partition_repsW.pl  1.1  11 years  overbeek  try
make_partition_reps.pl  1.1  11 years  overbeek  try
format_partition_dbs.pl  1.2  11 years  overbeek  try
compute_pins.pl  1.4  12 years  olson  undo bogus commit
initialize_ann_and_ev.pl  1.3  12 years  olson  undo bogus commit
svr_SAP.t  1.4  10 years  olson  update tests
connect_PDB_to_FIGfams_worker.pl  1.1  12 years  arodri7  update changes
make_figfam_tree.pl  1.1  12 years  arodri7  update changes
connect_PDB_to_FIGfams.pl  1.1  12 years  arodri7  update changes
test_figfam_peg.pl  1.6  12 years  arodri7  update changes
figfam_size_distribution.pl  1.1  12 years  arodri7  update changes
make_figfam_tree_worker.pl  1.1  12 years  arodri7  update changes
get_pubmed_journals.pl  1.5  13 years  hwang  update comment that this is for peg curation
update_SSU_rRNAs.pl  1.1  11 years  overbeek  update of SSUs
possible_frameshifts.pl  1.1  13 years  overbeek  update possible_frameshifts
svr_scripts.t  1.2  10 years  olson  updated tests
sims_between.pl  1.7  12 years  overbeek  updates on close connections
check_hope_info.pl  1.8  10 years  dejongh  updates to check for invalid maps and reaction/ec mismatches
run_find_subsys_against_all_genomes.pl  1.2  12 years  overbeek  updates to computation of VCs
load_id_correspondence.pl  1.3  12 years  olson  updates to the load_id_correspondence loader and searching code.
rapid_propagation.pl  1.75  11 years  olson  use $num_neighbors internally instead of hardwired constant
update_uniq_id_data.pl  1.7  13 years  olson  use function_of_quick
FFB2_get_prots.pl  1.2  10 years  overbeek  use only active genomes
crc64.py  1.1  12 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
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
wb.pl  1.1  10 years  overbeek  workbench for alignments and trees

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