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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).
function_of.pl  1.4  14 years  olson  Add license words.
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.
make_ncbi_files.pl  1.2  14 years  olson  Add license words.
run_start_predictions_for_all_subsystems.pl  1.4  14 years  olson  Add license words.
exclude_genomes.pl  1.2  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.
genome_peg_dna.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.
index_annotations.pl  1.9  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.
load_bbhs.pl  1.12  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.
connections_between.pl  1.2  14 years  olson  Add license words.
align_fasta.pl  1.2  14 years  olson  Add license words.
cluster_objects.pl  1.2  14 years  olson  Add license words.
check_lost_sims.pl  1.2  14 years  olson  Add license words.
flip_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.
assign_to_unchanged.pl  1.2  14 years  olson  Add license words.
make_attribute_index.pl  1.6  14 years  olson  Add license words.
filter_tbl_overlaps.pl  1.8  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.
build_nr_sources.pl  1.7  14 years  olson  Add license words.
clustal2fasta.pl  1.2  14 years  olson  Add license words.
check_subsystems.pl  1.4  14 years  olson  Add license words.
reformat_contigs.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.
backfill_gaps.pl  1.4  14 years  olson  Add license words.
add_rbs_data_for_start_predictions.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.
align_with_clustal_2.pl  1.3  14 years  olson  Add license words.
external_calls.pl  1.2  14 years  olson  Add license words.
make_close.pl  1.4  14 years  olson  Add license words.
gff2Ontology.pl  1.4  14 years  olson  Add license words.
update_uniq_id_data.pl  1.6  14 years  olson  Add license words.
compute_simple_scores.pl  1.4  14 years  olson  Add license words.
seed2pir.pl  1.2  14 years  olson  Add license words.
make_sp_func_syn_dicts.pl  1.2  14 years  olson  Add license words.
remove_clustered_pchs.pl  1.9  14 years  olson  Add license words.
pegs_in_conflict.pl  1.3  14 years  olson  Add license words.
order_corrections_for_start_predictions.pl  1.4  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.
get_fasta_for_tbl_entries.pl  1.5  14 years  olson  Add license words.
add_sim_data_for_start_predictions.pl  1.7  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.
split_and_trim_sequences.pl  1.10  14 years  olson  Add license words.
make_sp_uni_files.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.
get_dna.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.
make_indexes.pl  1.12  14 years  olson  Add license words.
extract_DNA_sequence_from_object_for_start_predictions.pl  1.2  14 years  olson  Add license words.
get_sims_for_start_predictions.pl  1.4  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.
reformat_sims.pl  1.6  14 years  olson  Add license words.
assess_completeness.pl  1.7  14 years  olson  Add license words.
map_sims.pl  1.5  14 years  olson  Add license words.
get_translations.pl  1.2  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.
load_sims.pl  1.9  14 years  olson  Add license words.
tips_of.pl  1.2  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.
fig_net.pl  1.3  14 years  olson  Add license words.
tabs2rel.pl  1.2  14 years  olson  Add license words.
verify_genome_directory.pl  1.26  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.
export_similarity_request.pl  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.
extract_sp_links.pl  1.2  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.
adjacent.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.
index_sims.pl  1.9  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.
index_subsystems.pl  1.7  14 years  olson  Add license words.
fix_eol.pl  1.2  14 years  olson  Add license words.
assign_to_close_strains.pl  1.7  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.
predict_starts.pl  1.7  14 years  olson  Add license words.
start_data_for_set_of_pegs.pl  1.5  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.
generate_similarities.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.
make_kegg_files.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.
compute_contig_md5.pl  1.3  14 years  olson  Add license words.
make_close_strain_data.pl  1.10  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.
get_ev_codes.pl  1.4  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.
runclustalw.pl  1.3  14 years  olson  Add license words.
backup_subsystems.pl  1.2  14 years  olson  Add license words.
trim_sequences.pl  1.6  14 years  olson  Add license words.
build_initial_objects_for_start_predictions.pl  1.10  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.
bielefeld_tarfile_to_seed.pl  1.4  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.
sort_and_split_bbhs.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.
load_pirsf.pl  1.10  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.
add_start_data_for_start_predictions.pl  1.3  14 years  olson  Add license words.
load_literature.pl  1.3  14 years  olson  Add license words.
check_sims_basic.pl  1.7  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.
map_pegs.pl  1.2  14 years  olson  Add license words.
load_peg_mapping.pl  1.7  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.
conditionally_assign.pl  1.3  14 years  olson  Add license words.
make_spreadsheet_and_notes.pl  1.3  14 years  olson  Add license words.
functionally_coupled.pl  1.5  14 years  olson  Add license words.
restore_assignments.pl  1.2  14 years  olson  Add license words.
load_coupling.pl  1.7  14 years  olson  Add license words.
Makefile  1.18  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.
blast2gff.pl  1.9  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.
get_potential_starts_for_start_predictions.pl  1.2  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.
pull_fasta_entries.pl  1.6  14 years  olson  Add license words.
compare_tbls.pl  1.3  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.
all_bbhs.pl  1.3  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.
make_sim_tab.pl  1.6  14 years  olson  Add license words.
pull_orfs.pl  1.3  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.
update_taxonomies.pl  1.7  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.
score_dfcs.pl  1.2  14 years  olson  Add license words.
check_sims_syntax.pl  1.3  14 years  olson  Add license words.
auto_assign.pl  1.16  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.
fig_specific_sequences.pl  1.2  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.
install-data.pl  1.7  14 years  olson  Add license words.
parse_genbank.pl  1.12  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.
extend_subsys.pl  1.6  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.
reduce_sims.pl  1.9  14 years  olson  Add license words.
generate_kernel_css.pl  1.5  14 years  olson  Add license words.
bayes_expected_start_scores.pl  1.2  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.
load_close.pl  1.7  14 years  olson  Add license words.
load_kegg.pl  1.7  14 years  olson  Add license words.
fig_rpc.pl  1.3  14 years  olson  Add license words.
make_calls.pl  1.4  14 years  olson  Add license words.
add_assertions_of_function.pl  1.31  14 years  olson  Add license words.
process_new_sims.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.
make_calls_for_start_predictions.pl  1.3  14 years  olson  Add license words.
import_subsystems.pl  1.22  14 years  olson  Add license words.
pegs_in_subsystems.pl  1.4  14 years  olson  Add license words.
sims_all.pl  1.2  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.
build_alignments_from_spreadsheet.pl  1.6  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.
direct_functional_coupling.pl  1.2  14 years  olson  Add license words.
load_sprout.pl  1.34  14 years  olson  Add license words.
build_nr.pl  1.15  14 years  olson  BIG BUG FIX. Sheesh, check in your fixes next time. sigh. --bob
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.
load_abstract_coupling.pl  1.3  14 years  parrello  Changed to use a single-character delimiter (for compatability with PostGRES).
index_translations.pl  1.17  14 years  golsen  Clearer interface to changing parameters, especially the length of the suffix us...
index_translation_files.c  1.4  14 years  golsen  Commit index_translation_files version 2.01 (use index_translation_files -v) Min...
diff_tbls.pl  1.1  14 years  overbeek  Computes difference betwween two tbl files. -- /gdp
load_attributes.pl  1.41  14 years  parrello  Converted to use "StandardSetup".
TransactFeatures.pl  1.18  14 years  parrello  Converted to use "StandardSetup".
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...
NMPDRAnalysis.pl  1.4  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...
TestLocations.pl  1.6  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...
Packager.pl  1.6  14 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
to_genbank.pl  1.3  14 years  overbeek  Fixed sorting bug. -- /gdp
index_pins.pl  1.1  14 years  olson  Index precomputed pins files.
sync_new_system.pl  1.6  14 years  golsen  Just adding a newline at end of file to make repository match my working copy. ...
add_to_alignment.pl  1.3  14 years  golsen  Make attempt to add a duplicate id nonfatal. Having the program die in the midd...
nmpdr2gff.pl  1.1  14 years  overbeek  RAE: Changes to gff3 files for NMPDR and adding nmpdr2gff for creating the files...
seed2gff.pl  1.13  14 years  overbeek  RAE: Changes to gff3 files for NMPDR and adding nmpdr2gff for creating the files...
make_fam_tabs.pl  1.5  14 years  overbeek  RAE: Protein Families interface and construction
fig.pl  1.100  14 years  overbeek  RAE: Swtiched to using SQL Count for the number of contigs
gff2tab.pl  1.2  14 years  overbeek  RAE: Updating GFF files for extracting data from TIGR
gff2seed.pl  1.22  14 years  overbeek  RAE: Updating GFF files for extracting data from TIGR
load_protein_families.pl  1.9  14 years  overbeek  RAE: extending protein families
init_FIG.pl  1.9  14 years  olson  SQLite support.
COPYING.TXT  1.1  14 years  olson  add license file
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
compute_sim_chunk.pl  1.3  14 years  olson  add working-on-chunk support
compute_pins.pl  1.1  14 years  olson  batch pin computation.
salvage_annotations.pl  1.6  14 years  olson  bugfix.
compute_genome_counts.pl  1.14  14 years  overbeek  changes to support dynamic sims and updates
extract_genomes.pl  1.38  14 years  overbeek  changes to support dynamic sims and updates
compute_potential_fusions.pl  1.12  14 years  overbeek  fix to fusions
index_contig_files.c  1.5  14 years  olson  fix to work on 64-bit linux
package_subsystems.pl  1.5  14 years  overbeek  fixes to deleted_features, replace_features_with, etc
load_features.pl  1.22  14 years  overbeek  fixes to deletion of features
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...
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
update_nr_cycle.pl  1.6  14 years  overbeek  load ext org table on update_nr_cycle
make_peg_maps.pl  1.3  14 years  overbeek  minor fixes
sims_between.pl  1.3  14 years  overbeek  minor fixes
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...
indirect_functional_coupling.pl  1.3  14 years  overbeek  update to computation of indirecdt functional coupling
score_ifcs.pl  1.3  14 years  overbeek  update to computation of indirecdt functional coupling

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