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File Rev. Age Author Last log entry
 Parent Directory        
COPYING.TXT  1.1  14 years  olson  add license file
Makefile  1.18  14 years  olson  Add license words.
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...
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...
README  1.1.1.1  16 years  efrank   import
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...
TransactFeatures.pl  1.18  14 years  parrello  Converted to use "StandardSetup".
add_assertions_of_function.pl  1.31  14 years  olson  Add license words.
add_assignments.pl  1.3  14 years  olson  Add license words.
add_close_genes.pl  1.2  14 years  olson  Add license words.
add_rbs_data_for_start_predictions.pl  1.2  14 years  olson  Add license words.
add_sim_data_for_start_predictions.pl  1.7  14 years  olson  Add license words.
add_start_data_for_start_predictions.pl  1.3  14 years  olson  Add license words.
add_to_alignment.pl  1.3  14 years  golsen  Make attempt to add a duplicate id nonfatal. Having the program die in the midd...
adjacent.pl  1.2  14 years  olson  Add license words.
ali_to_seq.pl  1.2  14 years  olson  Add license words.
alias2fig.pl  1.2  14 years  olson  Add license words.
aliases_of.pl  1.6  14 years  olson  Add license words.
align_fasta.pl  1.2  14 years  olson  Add license words.
align_with_clustal.pl  1.8  14 years  olson  Add license words.
align_with_clustal_2.pl  1.3  14 years  olson  Add license words.
all_bbhs.pl  1.3  14 years  olson  Add license words.
all_subsystems.pl  1.2  14 years  olson  Add license words.
alter_tbl.pl  1.4  14 years  olson  Add license words.
apply_map.pl  1.2  14 years  olson  Add license words.
apply_peg_changes_to_subsystem.pl  1.3  14 years  olson  Add license words.
are_close.pl  1.1  14 years  overbeek  fixes to extract_genomes
assess_completeness.pl  1.7  14 years  olson  Add license words.
assign.pl  1.2  14 years  olson  Add license words.
assign_synonym_ids.pl  1.2  14 years  olson  Add license words.
assign_synonym_ids_to_nr.pl  1.2  14 years  olson  Add license words.
assign_synonym_ids_to_sims.pl  1.2  14 years  olson  Add license words.
assign_to_close_strains.pl  1.7  14 years  olson  Add license words.
assign_to_hypo.pl  1.3  14 years  olson  Add license words.
assign_to_sets.pl  1.5  14 years  olson  Add license words.
assign_to_unchanged.pl  1.2  14 years  olson  Add license words.
assign_towards_subsystems.pl  1.2  14 years  olson  Add license words.
assign_with_no_sims.pl  1.2  14 years  olson  Add license words.
auto_assign.pl  1.16  14 years  olson  Add license words.
backfill_gaps.pl  1.4  14 years  olson  Add license words.
backup_critical_data.pl  1.4  14 years  olson  Add license words.
backup_subsystems.pl  1.2  14 years  olson  Add license words.
bayes_expected_start_scores.pl  1.2  14 years  olson  Add license words.
bbhs.pl  1.7  14 years  olson  Add license words.
best_hits.pl  1.2  14 years  olson  Add license words.
bielefeld_tarfile_to_seed.pl  1.4  14 years  olson  Add license words.
blast2gff.pl  1.9  14 years  olson  Add license words.
blast_request.pl  1.2  14 years  olson  Add license words.
blastn_seqs.pl  1.2  14 years  olson  Add license words.
blastp_pseq.pl  1.4  14 years  olson  Add license words.
boot_cluster_seed.pl  1.5  14 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
break_scaffolds.pl  1.2  14 years  olson  Add license words.
bring_system_up_to_date.pl  1.2  14 years  olson  Add license words.
build_access_sets.pl  1.2  14 years  olson  Add license words.
build_alignments_for_subsystems.pl  1.4  14 years  olson  Add license words.
build_alignments_from_spreadsheet.pl  1.6  14 years  olson  Add license words.
build_excel_gene_table.pl  1.3  14 years  olson  Add license words.
build_exemplar_fasta.pl  1.3  14 years  olson  Add license words.
build_initial_objects_for_start_predictions.pl  1.10  14 years  olson  Add license words.
build_nohit_fasta.pl  1.2  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
build_nr_sources.pl  1.7  14 years  olson  Add license words.
build_protein_families.pl  1.5  14 years  olson  Add license words.
build_syn.pl  1.2  14 years  olson  Add license words.
cat_spreadsheet.pl  1.2  14 years  olson  Add license words.
changed_starts.pl  1.7  14 years  olson  Add license words.
check_alignment.pl  1.2  14 years  olson  Add license words.
check_all_lost_sims.pl  1.2  14 years  olson  Add license words.
check_changes_in_organisms.pl  1.2  14 years  olson  Add license words.
check_fast_sims.pl  1.2  14 years  olson  Add license words.
check_for_unique_sims.pl  1.2  14 years  olson  Add license words.
check_lost_sims.pl  1.2  14 years  olson  Add license words.
check_nr_and_peg_synonyms.pl  1.2  14 years  olson  Add license words.
check_peg_assignments.pl  1.3  14 years  olson  Add license words.
check_sims_basic.pl  1.7  14 years  olson  Add license words.
check_sims_syntax.pl  1.3  14 years  olson  Add license words.
check_starts_for_peg_sets.pl  1.5  14 years  olson  Add license words.
check_starts_for_pegs.pl  1.5  14 years  olson  Add license words.
check_subsystems.pl  1.4  14 years  olson  Add license words.
check_tbl.pl  1.2  14 years  olson  Add license words.
clean_sims.pl  1.2  14 years  olson  Add license words.
clean_subsystems.pl  1.2  14 years  olson  Add license words.
clustal2fasta.pl  1.2  14 years  olson  Add license words.
clustal_to_fasta.pl  1.2  14 years  olson  Add license words.
cluster_by_bbhs.pl  1.2  14 years  olson  Add license words.
cluster_by_sim.pl  1.2  14 years  olson  Add license words.
cluster_objects.pl  1.2  14 years  olson  Add license words.
compare_tbls.pl  1.3  14 years  olson  Add license words.
compare_tree_and_alignment.pl  1.2  14 years  olson  Add license words.
complete_genomes.pl  1.7  14 years  olson  Add license words.
compute_changed_ids_for_nrs.pl  1.4  14 years  olson  Add license words.
compute_contig_md5.pl  1.3  14 years  olson  Add license words.
compute_dbdir_checksum.pl  1.3  14 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
compute_genome_counts.pl  1.14  14 years  overbeek  changes to support dynamic sims and updates
compute_new_ids.pl  1.2  14 years  olson  Add license words.
compute_pins.pl  1.1  14 years  olson  batch pin computation.
compute_pins_and_clusters.pl  1.2  14 years  olson  Add license words.
compute_potential_fusions.pl  1.12  14 years  overbeek  fix to fusions
compute_sim_chunk.pl  1.3  14 years  olson  add working-on-chunk support
compute_simple_scores.pl  1.4  14 years  olson  Add license words.
condense_blast.pl  1.2  14 years  olson  Add license words.
conditionally_assign.pl  1.3  14 years  olson  Add license words.
connections_between.pl  1.2  14 years  olson  Add license words.
count_bases.pl  1.2  14 years  olson  Add license words.
create_sims_btree.pl  1.1  14 years  olson  BTREE-index versions of these. Experimental still.
das_test.pl  1.2  14 years  olson  Add license words.
db_xrefs_of.pl  1.4  14 years  olson  Add license words.
delete_genomes_from_sims.pl  1.2  14 years  olson  Add license words.
diff_tbls.pl  1.1  14 years  overbeek  Computes difference betwween two tbl files. -- /gdp
direct_functional_coupling.pl  1.2  14 years  olson  Add license words.
display_tree.pl  1.4  14 years  olson  Add license words.
distribute_attributes.pl  1.11  14 years  olson  Add license words.
dna_seq.pl  1.2  14 years  olson  Add license words.
dump_attributes.pl  1.2  14 years  olson  Add license words.
dump_machine_state.pl  1.3  14 years  olson  Add license words.
embl2gff.pl  1.20  14 years  olson  Add license words.
embl2gff_addmd5.py  1.2  14 years  olson  Add license words.
exclude_genomes.pl  1.2  14 years  olson  Add license words.
expand_blast_table.pl  1.2  14 years  olson  Add license words.
expand_multifunctional_roles.pl  1.3  14 years  olson  Add license words.
expand_transferred_chunks.pl  1.4  14 years  olson  Add license words.
export_genome_as_gff.pl  1.6  14 years  olson  Add license words.
export_similarity_request.pl  1.2  14 years  olson  Add license words.
export_subsystem_as_gff.pl  1.2  14 years  olson  Add license words.
extend_subsys.pl  1.6  14 years  olson  Add license words.
extend_subsystem.pl  1.2  14 years  olson  Add license words.
external_calls.pl  1.2  14 years  olson  Add license words.
extract_DNA_for_whole_ORFs.pl  1.3  14 years  olson  Add license words.
extract_DNA_sequence_from_object_for_start_predictions.pl  1.2  14 years  olson  Add license words.
extract_data_for_syncing_after_update.pl  1.6  14 years  olson  Add license words.
extract_data_to_keep.pl  1.5  14 years  olson  Add license words.
extract_genes.pl  1.5  14 years  olson  Add license words.
extract_genomes.pl  1.38  14 years  overbeek  changes to support dynamic sims and updates
extract_sp_links.pl  1.2  14 years  olson  Add license words.
extract_subset_from_sprout_data.pl  1.2  14 years  olson  Add license words.
fasta_cksum.c  1.4  14 years  olson  Doh, put proper comments in for C code.
fasta_for_hypo.pl  1.2  14 years  olson  Add license words.
fasta_to_phylip.pl  1.2  14 years  olson  Add license words.
fastasize.c  1.3  14 years  olson  Doh, put proper comments in for C code.
fid2dna.pl  1.2  14 years  olson  Add license words.
fig.pl  1.100  14 years  overbeek  RAE: Swtiched to using SQL Count for the number of contigs
fig_net.pl  1.3  14 years  olson  Add license words.
fig_rpc.pl  1.3  14 years  olson  Add license words.
fig_specific_sequences.pl  1.2  14 years  olson  Add license words.
fig_xmlrpc_server.pl  1.5  14 years  olson  Add license words.
fill_in_cell.pl  1.2  14 years  olson  Add license words.
fill_in_roles.pl  1.4  14 years  olson  Add license words.
fill_subsys.pl  1.5  14 years  olson  Add license words.
filter_new_overlaps.pl  1.2  14 years  olson  Add license words.
filter_pegs_in_subsystems.pl  1.4  14 years  olson  Add license words.
filter_tbl_overlaps.pl  1.8  14 years  olson  Add license words.
find_maximal_clusters.pl  1.2  14 years  olson  Add license words.
fix_annotations.pl  1.2  14 years  olson  Add license words.
fix_eol.pl  1.2  14 years  olson  Add license words.
fix_ext_funcs.pl  1.2  14 years  olson  Add license words.
flatten_fasta.pl  1.1  14 years  overbeek  add some minor utilities to flatten/unflatten fasta files
flattened_to_fasta.pl  1.1  14 years  overbeek  add some minor utilities to flatten/unflatten fasta files
flip_sims.pl  1.2  14 years  olson  Add license words.
format_peg_dbs.pl  1.3  14 years  olson  Add license words.
function_of.pl  1.4  14 years  olson  Add license words.
functionally_coupled.pl  1.5  14 years  olson  Add license words.
fusion_of.pl  1.2  14 years  olson  Add license words.
gather_attributes.pl  1.8  14 years  olson  Add license words.
genbank2gff3.pl  1.5  14 years  olson  Add license words.
generate_GenomeGroups_for_sprout.pl  1.3  14 years  olson  Add license words.
generate_Property_for_sprout.pl  1.6  14 years  olson  Add license words.
generate_Source_for_sprout.pl  1.2  14 years  olson  Add license words.
generate_gene_blocks.pl  1.3  14 years  olson  Add license words.
generate_genome_feature_tables_for_sprout.pl  1.16  14 years  olson  Add license words.
generate_input_for_auto_assignments.pl  1.2  14 years  olson  Add license words.
generate_intergenic_blocks.pl  1.3  14 years  olson  Add license words.
generate_kernel_css.pl  1.5  14 years  olson  Add license words.
generate_max_clusters.pl  1.2  14 years  olson  Add license words.
generate_pin_caches.pl  1.5  14 years  olson  Add license words.
generate_pinned_homologs.pl  1.2  14 years  olson  Add license words.
generate_similarities.pl  1.2  14 years  olson  Add license words.
generate_sprout_links.pl  1.2  14 years  olson  Add license words.
generate_subsys_tables_for_sprout.pl  1.8  14 years  olson  Add license words.
genome_peg_dna.pl  1.2  14 years  olson  Add license words.
genomes_of.pl  1.2  14 years  olson  Add license words.
get_best_set_of_genes_for_column.pl  1.3  14 years  olson  Add license words.
get_class_examples.pl  1.2  14 years  olson  Add license words.
get_dna.pl  1.3  14 years  olson  Add license words.
get_empty_ecs  1.3  14 years  olson  Add license words.
get_empty_ecs.pl  1.4  14 years  olson  Add license words.
get_ev_codes.pl  1.4  14 years  olson  Add license words.
get_fasta_for_tbl_entries.pl  1.5  14 years  olson  Add license words.
get_long_enough.pl  1.2  14 years  olson  Add license words.
get_nr_entries_without_sims.pl  1.4  14 years  olson  Add license words.
get_pathways_for_EC.pl  1.2  14 years  olson  Add license words.
get_potential_starts_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.
get_translations.pl  1.2  14 years  olson  Add license words.
gff2Ontology.pl  1.4  14 years  olson  Add license words.
gff2seed.pl  1.22  14 years  overbeek  RAE: Updating GFF files for extracting data from TIGR
gff2tab.pl  1.2  14 years  overbeek  RAE: Updating GFF files for extracting data from TIGR
gi2fig.pl  1.3  14 years  olson  Add license words.
html_parser.py  1.2  14 years  olson  Add license words.
import_external_sequences_step1.pl  1.8  14 years  olson  Add license words.
import_external_sequences_step3.pl  1.5  14 years  olson  Add license words.
import_subsystems.pl  1.22  14 years  olson  Add license words.
index_annotations.pl  1.9  14 years  olson  Add license words.
index_contig_files.c  1.5  14 years  olson  fix to work on 64-bit linux
index_contigs.pl  1.11  14 years  olson  Add license words.
index_fasta.pl  1.2  14 years  olson  Add license words.
index_neighborhoods.pl  1.3  14 years  olson  Add license words.
index_pins.pl  1.1  14 years  olson  Index precomputed pins files.
index_sims.pl  1.9  14 years  olson  Add license words.
index_sims_file.c  1.3  14 years  olson  Doh, put proper comments in for C code.
index_sprout.pl  1.12  14 years  olson  Add license words.
index_subsystems.pl  1.7  14 years  olson  Add license words.
index_translation_files.c  1.4  14 years  golsen  Commit index_translation_files version 2.01 (use index_translation_files -v) Min...
index_translations.pl  1.17  14 years  golsen  Clearer interface to changing parameters, especially the length of the suffix us...
indirect_functional_coupling.pl  1.3  14 years  overbeek  update to computation of indirecdt functional coupling
init_FIG.pl  1.9  14 years  olson  SQLite support.
init_dbserver.pl  1.3  14 years  olson  Add license words.
init_maps.pl  1.3  14 years  olson  Add license words.
init_peg_job_scheduler.pl  1.4  14 years  olson  Add license words.
initial_set.pl  1.2  14 years  olson  Add license words.
initialize_alignments_for_subsystems.pl  1.2  14 years  overbeek  fixes to extract_genomes, salvage_subsystem_rows and initialize_alignments_for_s...
insert.pl  1.2  14 years  olson  Add license words.
insert_all.pl  1.2  14 years  olson  Add license words.
install-data.pl  1.7  14 years  olson  Add license words.
install_annotations.pl  1.4  14 years  olson  Add license words.
install_assignments.pl  1.7  14 years  olson  Add license words.
install_code.pl  1.2  14 years  olson  Add license words.
install_feature_updates.pl  1.2  14 years  olson  Add license words.
install_lightweight_code.pl  1.2  14 years  olson  Add license words.
install_subsystems.pl  1.2  14 years  olson  Add license words.
install_translation_rules.pl  1.3  14 years  olson  Add license words.
interval.pl  1.2  14 years  olson  Add license words.
is_archaeal.pl  1.2  14 years  olson  Add license words.
is_bacterial.pl  1.2  14 years  olson  Add license words.
is_eukaryotic.pl  1.2  14 years  olson  Add license words.
is_prokaryotic.pl  1.2  14 years  olson  Add license words.
keep_only.pl  1.2  14 years  olson  Add license words.
lengths_of_contigs.pl  1.2  14 years  olson  Add license words.
list_genomes.pl  1.2  14 years  olson  Add license words.
load_abstract_coupling.pl  1.3  14 years  parrello  Changed to use a single-character delimiter (for compatability with PostGRES).
load_attributes.pl  1.41  14 years  parrello  Converted to use "StandardSetup".
load_bbhs.pl  1.12  14 years  olson  Add license words.
load_bbhs_btree.pl  1.1  14 years  olson  BTREE-index versions of these. Experimental still.
load_chromosomal_clusters.pl  1.2  14 years  olson  Add license words.
load_close.pl  1.7  14 years  olson  Add license words.
load_coupling.pl  1.7  14 years  olson  Add license words.
load_coupling_btree.pl  1.1  14 years  olson  BTREE-index versions of these. Experimental still.
load_distances.pl  1.5  14 years  olson  Add license words.
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...
load_external_orgs.pl  1.3  14 years  olson  Add license words.
load_features.pl  1.22  14 years  overbeek  fixes to deletion of features
load_hugo.pl  1.6  14 years  olson  Add license words.
load_kegg.pl  1.7  14 years  olson  Add license words.
load_links.pl  1.6  14 years  olson  Add license words.
load_literature.pl  1.3  14 years  olson  Add license words.
load_local_maps.pl  1.3  14 years  olson  Add license words.
load_pch_pins.pl  1.2  14 years  olson  Add license words.
load_peg_mapping.pl  1.7  14 years  olson  Add license words.
load_pirsf.pl  1.10  14 years  olson  Add license words.
load_protein_families.pl  1.9  14 years  overbeek  RAE: extending protein families
load_sets.pl  1.5  14 years  olson  Add license words.
load_sims.pl  1.9  14 years  olson  Add license words.
load_sprout.pl  1.34  14 years  olson  Add license words.
location_of.pl  1.2  14 years  olson  Add license words.
make_PHOBs_for_subsystems.pl  1.5  14 years  olson  Add license words.
make_annotations_for_sprout.pl  1.12  14 years  olson  Add license words.
make_assignments_fit_initial_css.pl  1.4  14 years  olson  Add license words.
make_assignments_set.pl  1.3  14 years  olson  Add license words.
make_attribute_index.pl  1.6  14 years  olson  Add license words.
make_binary.pl  1.2  14 years  olson  Add license words.
make_calls.pl  1.4  14 years  olson  Add license words.
make_calls_for_start_predictions.pl  1.3  14 years  olson  Add license words.
make_close.pl  1.4  14 years  olson  Add license words.
make_close_strain_data.pl  1.10  14 years  olson  Add license words.
make_fam_tabs.pl  1.5  14 years  overbeek  RAE: Protein Families interface and construction
make_fig_files.pl  1.3  14 years  olson  Add license words.
make_indexes.pl  1.12  14 years  olson  Add license words.
make_jpg.pl  1.2  14 years  olson  Add license words.
make_kegg_files.pl  1.2  14 years  olson  Add license words.
make_maps_from_sub.py  1.5  14 years  olson  Add license words.
make_match_table.pl  1.2  14 years  olson  Add license words.
make_ncbi_files.pl  1.2  14 years  olson  Add license words.
make_occ_counts.pl  1.2  14 years  olson  Add license words.
make_peg_maps.pl  1.3  14 years  overbeek  minor fixes
make_phob_from_ids.pl  1.3  14 years  olson  Add license words.
make_phob_from_seqs.pl  1.7  14 years  olson  Add license words.
make_protein_sets.pl  1.4  14 years  olson  Add license words.
make_rates.pl  1.2  14 years  olson  Add license words.
make_sim_sets.pl  1.3  14 years  olson  Add license words.
make_sim_tab.pl  1.6  14 years  olson  Add license words.
make_sp_desc_with_org.pl  1.2  14 years  olson  Add license words.
make_sp_func_syn_dicts.pl  1.2  14 years  olson  Add license words.
make_sp_org_domain_table.pl  1.2  14 years  olson  Add license words.
make_sp_org_table.pl  1.2  14 years  olson  Add license words.
make_sp_uni_files.pl  1.2  14 years  olson  Add license words.
make_spreadsheet_and_notes.pl  1.3  14 years  olson  Add license words.
make_sprout_bbhs.pl  1.2  14 years  olson  Add license words.
make_sprout_upstream.pl  1.2  14 years  olson  Add license words.
make_subsystems_from_clusters.pl  1.5  14 years  olson  Add license words.
make_transferable_chunks.pl  1.4  14 years  olson  Add license words.
make_transferable_tarfiles.pl  1.3  14 years  olson  Add license words.
map_pegs.pl  1.2  14 years  olson  Add license words.
map_sims.pl  1.5  14 years  olson  Add license words.
map_sims_for_bigfc.pl  1.2  14 years  olson  Add license words.
mark_nr.pl  1.2  14 years  olson  Add license words.
match_dna_to_aligned_prots.pl  1.4  14 years  olson  Add license words.
md5.c  1.3  14 years  olson  Doh, put proper comments in for C code.
merge_annotations.pl  1.3  14 years  olson  Add license words.
merge_translation_rules.pl  1.7  14 years  olson  Add license words.
nmpdr2gff.pl  1.1  14 years  overbeek  RAE: Changes to gff3 files for NMPDR and adding nmpdr2gff for creating the files...
order_corrections_for_start_predictions.pl  1.4  14 years  olson  Add license words.
order_sets.pl  1.3  14 years  olson  Add license words.
p2p_daemon.pl  1.2  14 years  olson  Add license words.
p2p_sync_cron.pl  1.3  14 years  olson  Add license words.
p2p_sync_from_remote.pl  1.4  14 years  olson  Add license words.
package_annotations.pl  1.9  14 years  olson  Add license words.
package_assignments.pl  1.8  14 years  olson  Add license words.
package_code.pl  1.2  14 years  olson  Add license words.
package_lightweight_code.pl  1.2  14 years  olson  Add license words.
package_raw_data_for_transplant.pl  1.2  14 years  olson  Add license words.
package_sims.pl  1.2  14 years  olson  Add license words.
package_subsystems.pl  1.5  14 years  overbeek  fixes to deleted_features, replace_features_with, etc
package_translation_rules.pl  1.2  14 years  olson  Add license words.
paint_tree.pl  1.3  14 years  olson  Add license words.
parse_genbank.pl  1.12  14 years  olson  Add license words.
parse_mart.py  1.6  14 years  olson  Add license words.
peg_to_name.pl  1.4  14 years  olson  Add license words.
peg_to_pdb.py  1.2  14 years  olson  Add license words.
peg_to_subsystems.pl  1.3  14 years  olson  Add license words.
pegs.pl  1.3  14 years  olson  Add license words.
pegs_in_conflict.pl  1.3  14 years  olson  Add license words.
pegs_in_subsystem.pl  1.5  14 years  olson  Add license words.
pegs_in_subsystems.pl  1.4  14 years  olson  Add license words.
possibly_truncated.pl  1.2  14 years  olson  Add license words.
postprocess_computed_sims.pl  1.2  14 years  olson  Add license words.
potentially_cotranscribed.pl  1.2  14 years  olson  Add license words.
pp.pl  1.3  14 years  olson  Add license words.
predict_starts.pl  1.7  14 years  olson  Add license words.
prep_viz.pl  1.2  14 years  olson  Add license words.
process_new_sims.pl  1.4  14 years  olson  Add license words.
process_sim_deletions_and_replacements.pl  1.3  14 years  olson  Add license words.
project.pl  1.2  14 years  olson  Add license words.
pull_fasta_entries.pl  1.6  14 years  olson  Add license words.
pull_orfs.pl  1.3  14 years  olson  Add license words.
pull_sp_entries.pl  1.2  14 years  olson  Add license words.
put_directory_in_one_file.pl  1.2  14 years  olson  Add license words.
questionable_calls.pl  1.2  14 years  olson  Add license words.
rationalize_blast.pl  1.3  14 years  olson  Add license words.
reduce_sims.pl  1.9  14 years  olson  Add license words.
reformat_contigs.pl  1.2  14 years  olson  Add license words.
reformat_dsim_dbs.pl  1.2  14 years  olson  Add license words.
reformat_fasta.pl  1.2  14 years  olson  Add license words.
reformat_sims.pl  1.6  14 years  olson  Add license words.
register_features_batch.pl  1.2  14 years  olson  Add license words.
register_features_with_clearinghouse.pl  1.2  14 years  olson  Add license words.
relabel_nodes.pl  1.2  14 years  olson  Add license words.
relevant_PCHs.pl  1.3  14 years  olson  Add license words.
relevant_pchsG.pl  1.4  14 years  olson  Add license words.
remove_clustered_pchs.pl  1.9  14 years  olson  Add license words.
renumber_seed_dir.pl  1.2  14 years  olson  Add license words.
report_changes.pl  1.2  14 years  olson  Add license words.
representative_tree.pl  1.2  14 years  olson  Add license words.
restore_annotations.pl  1.2  14 years  olson  Add license words.
restore_assignments.pl  1.2  14 years  olson  Add license words.
restore_translation_rules.pl  1.2  14 years  olson  Add license words.
restrict_by_similarity.pl  1.4  14 years  olson  Add license words.
restrict_to_genomes.pl  1.3  14 years  olson  Add license words.
roles_in_subsystem.pl  1.2  14 years  olson  Add license words.
root_at.pl  1.2  14 years  olson  Add license words.
run_fc.pl  1.2  14 years  olson  Add license words.
run_peg_job_worker.pl  1.4  14 years  olson  Add license words.
run_start_predictions_for_all_subsystems.pl  1.4  14 years  olson  Add license words.
run_start_predictions_for_spreadsheet.pl  1.6  14 years  olson  Add license words.
runclustalw.pl  1.3  14 years  olson  Add license words.
salvage_annotations.pl  1.6  14 years  olson  bugfix.
salvage_master_annotations.pl  1.3  14 years  overbeek  fixes to salvage code
salvage_subsystem_rows.pl  1.6  14 years  overbeek  fixes to salvage code
same_subsys.pl  1.1  14 years  overbeek  fixes to extract_genomes
score_dfcs.pl  1.2  14 years  olson  Add license words.
score_ifcs.pl  1.3  14 years  overbeek  update to computation of indirecdt functional coupling
seed2gff.pl  1.13  14 years  overbeek  RAE: Changes to gff3 files for NMPDR and adding nmpdr2gff for creating the files...
seed2pir.pl  1.2  14 years  olson  Add license words.
seed_job_scheduler.pl  1.3  14 years  olson  Add license words.
select_genomes_for_sprout.pl  1.2  14 years  olson  Add license words.
set_to_relation.pl  1.2  14 years  olson  Add license words.
show_reconfig_cmd.pl  1.3  14 years  olson  Add license words.
similar_to.pl  1.4  14 years  olson  Add license words.
sims_all.pl  1.2  14 years  olson  Add license words.
sims_between.pl  1.3  14 years  overbeek  minor fixes
sort_and_split_bbhs.pl  1.4  14 years  olson  Add license words.
sp2fasta.pl  1.2  14 years  olson  Add license words.
split_and_install_pchs.pl  1.2  14 years  olson  Add license words.
split_and_trim_sequences.pl  1.10  14 years  olson  Add license words.
split_sims.pl  1.3  14 years  olson  Add license words.
splitup.pl  1.4  14 years  olson  Add license words.
sprout_search.pl  1.2  14 years  olson  Add license words.
start_data_for_set_of_pegs.pl  1.5  14 years  olson  Add license words.
start_dbserver.pl  1.2  14 years  olson  Add license words.
start_services.pl  1.12  14 years  olson  Add license words.
stop_services.pl  1.5  14 years  olson  Add license words.
subtree_of.pl  1.2  14 years  olson  Add license words.
sync_new_system.pl  1.6  14 years  golsen  Just adding a newline at end of file to make repository match my working copy. ...
synchronize_annotations_and_assignments.pl  1.2  14 years  olson  Add license words.
tabs2rel.pl  1.2  14 years  olson  Add license words.
test_cv.expected  1.1  14 years  efrank   Basic regression test on CV stuff at FIG API level (which underlies CGI).
test_cv.pl  1.2  14 years  olson  Add license words.
test_generate_anno_gff.pl  1.3  14 years  olson  Add license words.
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...
tips_of.pl  1.2  14 years  olson  Add license words.
to_genbank.pl  1.3  14 years  overbeek  Fixed sorting bug. -- /gdp
to_gg.pl  1.2  14 years  olson  Add license words.
to_gids.pl  1.2  14 years  olson  Add license words.
to_insert.pl  1.2  14 years  olson  Add license words.
to_map_coords.pl  1.3  14 years  olson  Add license words.
translate.pl  1.2  14 years  olson  Add license words.
translation_of.pl  1.2  14 years  olson  Add license words.
trim_sequences.pl  1.6  14 years  olson  Add license words.
uninstall.pl  1.2  14 years  olson  Add license words.
uninstall.sims.pl  1.2  14 years  olson  Add license words.
update_nr_cycle.pl  1.6  14 years  overbeek  load ext org table on update_nr_cycle
update_sims.pl  1.13  14 years  olson  Add license words.
update_taxonomies.pl  1.7  14 years  olson  Add license words.
update_uniq_id_data.pl  1.6  14 years  olson  Add license words.
upstream.pl  1.3  14 years  olson  Add license words.
validate_genome_gff.pl  1.6  14 years  olson  Add license words.
validate_subsystem.pl  1.2  14 years  olson  Add license words.
verify_genome_directory.pl  1.26  14 years  olson  Add license words.
verify_pegs_in_tbl.pl  1.2  14 years  olson  Add license words.
where_does_seq_hit.pl  1.2  14 years  olson  Add license words.

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