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File (rev) Rev. Age Author Last log entry
 Parent Directory        
write_go_mappings.pl  1.2  8 years  olson  More fixups.
where_does_seq_hit.pl  1.2  14 years  olson  Add license words.
wb.pl  1.1  9 years  overbeek  workbench for alignments and trees
verify_pegs_in_tbl.pl  1.2  14 years  olson  Add license words.
verify_genome_directory.pl  1.42  8 years  gdpusch  Added recognition of "contig.properties" file.
validate_subsystem.pl  1.2  14 years  olson  Add license words.
validate_genome_gff.pl  1.6  14 years  olson  Add license words.
validate_fasta.pl  1.1  12 years  redwards  Initial release of programs to check and fix valid fasta format
valid_fasta_file.pl  1.1  9 years  olson  Check to ensure a fasta file is valid.
upstream.pl  1.3  14 years  olson  Add license words.
uproot.pl  1.1  12 years  overbeek  add uproot
update_uniq_id_data.pl  1.7  12 years  olson  use function_of_quick
update_taxonomies.pl  1.8  13 years  overbeek  set longer gap between accessing NCBI
update_sims2.pl  1.6  9 years  olson  updated code
update_sims.pl  1.13  14 years  olson  Add license words.
update_nr_cycle.pl  1.6  13 years  overbeek  load ext org table on update_nr_cycle
update_lineage.pl  1.3  11 years  wilke  draft version to update FIG taxonomy entries
update_kegg_data.pl  1.6  9 years  dejongh  removed comment
update_hope_info.pl  1.4  9 years  dejongh  added comments
update_fr2go.pl  1.1  13 years  overbeek  put in the fr2go stuff
update_SSU_rRNAs.pl  1.1  10 years  overbeek  update of SSUs
update_PSEED_subsystems.pl  1.3  9 years  olson  add doc
update_OTUs.pl  1.5  8 years  overbeek  fix OTU update to use gary olsen sequence grouping script
update_FIGfams.pl  1.12  10 years  arodri7  commit changes
update-caches.pl  1.1  12 years  olson  Update SEED caches.
uninstall.sims.pl  1.2  14 years  olson  Add license words.
uninstall.pl  1.2  14 years  olson  Add license words.
uni_lit_to_dlits.pl  1.1  11 years  overbeek  dlit support
trimmed_kernel_alignment.pl  1.1  12 years  overbeek  add last round of phylogeny tools
trim_sequences.pl  1.11  10 years  overbeek  fixes bug in handling multidomain prots
trim_alignment.pl  1.2  12 years  overbeek  minor fixes
translation_of.pl  1.2  14 years  olson  Add license words.
translate.pl  1.2  14 years  olson  Add license words.
track_figfams.pl  1.2  13 years  overbeek  get rid of diagnostics in track_figfams
trace.pl  1.3  11 years  parrello  Fixed so that the destination is not case-sensitive.
to_structured_english.pl  1.1  11 years  overbeek  add routine to build structured english rendering of evidence codes
to_prodom.pl  1.7  10 years  olson  fix updated URL
to_org_specific.pl  1.4  13 years  hwang  fix syntax error
to_map_coords.pl  1.3  14 years  olson  Add license words.
to_insert.pl  1.2  14 years  olson  Add license words.
to_gids.pl  1.2  14 years  olson  Add license words.
to_gg.pl  1.2  14 years  olson  Add license words.
to_genbank.pl  1.7  9 years  gdpusch  Fixed bug handling 5S.
to_arabidopsis.pl  1.1  12 years  hwang  This script parses arabidopsis.org to get the AT aliases output
tips_of.pl  1.3  12 years  overbeek  add insert_prot_into_tree, a new way to insert proteins into a tree
test_placement.pl  1.1  12 years  overbeek  redone FIGfam stuff
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...
test_generate_anno_gff.pl  1.3  14 years  olson  Add license words.
test_figfam_placement_into_families.pl  1.10  9 years  disz  FigFam 6 digit problem
test_figfam_peg.pl  1.6  11 years  arodri7  update changes
test_figfam_FF_peg.pl  1.3  11 years  olson  Missed one of the figfamdata fixes.
test_cv.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_Observation.pl  1.1  12 years  mkubal  for testing
tabs2rel.pl  1.2  14 years  olson  Add license words.
synchronize_annotations_and_assignments.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. ...
svr_with_close_blast_hits.pl  1.1  9 years  overbeek  a utility to find close hits
svr_upstream.pl  1.8  9 years  parrello  More server script stuff. Thought I'd already installed these last week...
svr_update_assignments.pl  1.3  9 years  gdpusch  Fixed typo.
svr_trim_ali.pl  1.10  8 years  fangfang  fix description field in trim html
svr_tree_to_html.pl  1.11  8 years  fangfang  newicklib
svr_tree.pl  1.10  8 years  fangfang  add parallel support for bootstrap
svr_translations_of.pl  1.6  8 years  golsen  Add an option of genome names in the output. Clean up the way functions are adde...
svr_tips_of_tree.pl  1.2  9 years  overbeek  add correspondence translation
svr_taxonomy.pl  1.2  9 years  disz  FIxed POD
svr_taxonomically_related_genomes.pl  1.10  8 years  fangfang  update POD
svr_tab2html.pl  1.5  9 years  gdpusch  Fixed a bug I introduced, and added a "--border" option to the table.
svr_summarize_protein_families.pl  1.2  9 years  overbeek  minor changes
svr_summarize_contigs.pl  1.2  9 years  parrello  New script, some documentation fixes.
svr_summarize_MG_output.pl  1.4  9 years  overbeek  extend the number of digits in the fraction of the total
svr_subsystem_spreadsheet.pl  1.1  9 years  parrello  subsystem download scripts.
svr_subsystem_roles.pl  1.2  8 years  overbeek  allow ss from stdin
svr_subsystem_genomes.pl  1.1  9 years  parrello  Discrimination functions support scripts.
svr_subsystem_genome_data.pl  1.1  9 years  parrello  More server scripts.
svr_submit_correspondences.pl  1.1  9 years  parrello  First round of script updates & additions for tutorial.
svr_submit_RAST_job.pl  1.13  9 years  gdpusch  Added default value for bioname.
svr_status_of_RAST_job.pl  1.4  9 years  olson  add url argument
svr_ss_classes.pl  1.1  8 years  parrello  Added to get classification data for subsystems.
svr_spreadsheet_to_file.pl  1.2  8 years  disz  Fixed missing file error message
svr_split_fams.pl  1.1  9 years  overbeek  minor changes
svr_sketch_tree.pl  1.1  9 years  overbeek  slightly modified version of the older sketch_tree
svr_sims2html.pl  1.6  9 years  golsen  Add pod documentation.
svr_similar_to.pl  1.2  9 years  parrello  Fixed POD errors.
svr_seed_to_table.pl  1.3  9 years  gdpusch  Fixed typo in POD section.
svr_seed_to_genbank.pl  1.2  8 years  gdpusch  Fixed use of "package" when I meant "use." :(
svr_scripts.t  1.2  10 years  olson  updated tests
svr_scanP.pl  1.2  8 years  overbeek  add a little documentation
svr_scanN.pl  1.1  8 years  overbeek  scanning utilities
svr_run_RAST_jobs.pl  1.6  9 years  olson  Add --determineFamily
svr_roles_to_subsys.pl  1.1  9 years  parrello  Added "roles_to_subsys", sped up "figfams_to_ids", fixed pod for "mapped_genomes...
svr_roles_to_reactions.pl  1.1  8 years  parrello  New script for reactions of roles.
svr_role_to_pegs.pl  1.3  8 years  overbeek  mispelled genome with bad consequences
svr_retrieve_RAST_job.pl  1.3  10 years  olson  Misc server fixes
svr_reroot_tree.pl  1.3  9 years  overbeek  fix typo
svr_representative_sequences.pl  1.1  9 years  overbeek  keep representative_sequences, but make it a shadow of the new svr_representativ...
svr_rep_seqs.pl  1.2  9 years  overbeek  add SAS component
svr_reactions_to_roles.pl  1.1  8 years  parrello  New chemistry-based scripts.
svr_reactions_in_model.pl  1.1  8 years  parrello  New script for Ross.
svr_reaction_description.pl  1.3  8 years  parrello  Added -f flag.
svr_rRNA.pl  1.2  8 years  fangfang  update pod
svr_psiblast_search.pl  1.23  8 years  fangfang  add -a n_processor option
svr_protein_assertions.pl  1.6  9 years  disz  CHanged ACHserver to SAPserver and fixed processing of return values
svr_possible_joins.pl  1.1  9 years  overbeek  tools to try to bridge contigs
svr_pegs_in_subsystems.pl  1.7  8 years  parrello  Fixed to process 10 subsystems at a time, reducing the chances of a timeout.
svr_otus.pl  1.3  9 years  overbeek  minor fixes
svr_oligomer_similarity.pl  1.1  9 years  overbeek  compute oligo similarities
svr_neighbors_of.pl  1.3  9 years  parrello  Fixed POD errors. Added examples.
svr_neighboring_reactions.pl  1.2  8 years  overbeek  minor fixes
svr_neighborhood_of_role.pl  1.3  8 years  parrello  Converted to use chemistry data instead of the models.
svr_motif.pl  1.4  8 years  fangfang  simplify code
svr_missing_roles.pl  1.2  8 years  overbeek  added -g genome
svr_metabolic_reconstruction.pl  1.5  9 years  olson  bah, fix paste error
svr_members_of_otu.pl  1.3  9 years  parrello  Added support for specifying input IDs on the command line.
svr_md5_of_prot.pl  1.1  8 years  overbeek  get md5s for pegs
svr_mapped_genomes.pl  1.3  9 years  parrello  Added "roles_to_subsys", sped up "figfams_to_ids", fixed pod for "mapped_genomes...
svr_make_pan_genome_prot_families.pl  1.7  9 years  overbeek  parallelize computation of correspondnece tables
svr_location_of.pl  1.1  8 years  parrello  Added due to seminar user request.
svr_kill_RAST_job.pl  1.4  10 years  olson  fix usage message
svr_keep_only.pl  1.1  9 years  overbeek  support filtering on function or role
svr_just_ends.pl  1.3  8 years  redwards  increasing min length to 2000 so that you have two ends!
svr_is_hypo.pl  1.3  8 years  overbeek  minor fixes
svr_intergenic_regions.pl  1.1  9 years  parrello  New script to find intergenic regions.
svr_insert_seqs_into_alignment.pl  1.2  9 years  fangfang  take advantage of gjoseqlib's flexible API to implicitly interact with STDIN/STD...
svr_inherit_annotations.pl  1.2  8 years  gdpusch  Checkin of (hopefully) production version
svr_inherit_aliases.pl  1.1  8 years  overbeek  inherit aliases
svr_in_runs.pl  1.5  9 years  parrello  Fixed POD errors. Added examples.
svr_ids_to_subsystems.pl  1.6  9 years  disz  Added stderr output for non-matches
svr_ids_to_figfams.pl  1.8  9 years  overbeek  fixes to documentation
svr_get_coupling_data.pl  1.2  8 years  overbeek  must have -d
svr_genome_statistics.pl  1.2  9 years  parrello  Added genome name to the POD.
svr_genome_functions.pl  1.3  9 years  overbeek  sort by feature id
svr_gene_data.pl  1.3  9 years  parrello  First round of script updates & additions for tutorial.
svr_genbank_to_table.pl  1.2  9 years  gdpusch  Added various alias IDs to output.
svr_genbank_to_seed.pl  1.1  8 years  gdpusch  SVR GenBank parser using Gary\'s code
svr_gap_filled_reactions_and_roles.pl  1.4  8 years  overbeek  fix reference to FBAmodels
svr_functionally_coupled.pl  1.2  8 years  overbeek  add cutoffs
svr_function_of.pl  1.9  8 years  overbeek  handle empty input
svr_find_regulatory_proteins.pl  1.1  9 years  overbeek  a simple tool to find potential regulatory proteins
svr_find_hypos_for_cluster.pl  1.1  8 years  overbeek  find hypotheticals associated with clusters
svr_find_clusters_relevant_to_reaction.pl  1.4  8 years  overbeek  fixes relating to use of packages
svr_file_to_spreadsheet.pl  1.2  8 years  disz  Fixed error message
svr_figfams_to_ids.pl  1.6  9 years  parrello  Added "roles_to_subsys", sped up "figfams_to_ids", fixed pod for "mapped_genomes...
svr_figfam_functions.pl  1.2  9 years  parrello  Added option to get all the FIGfams.
svr_figfam_fasta.pl  1.5  9 years  parrello  More server script stuff. Thought I'd already installed these last week...
svr_fig_id_corr.pl  1.4  10 years  overbeek  add -precise option
svr_fc_figfams.pl  1.3  9 years  overbeek  sort by score
svr_fasta.pl  1.14  8 years  overbeek  wrap the seq into 60-char lines
svr_expressed_genes_in_range.pl  1.1  8 years  parrello  Added for looking at genes that are never or always expressed.
svr_exp_genomes.pl  1.1  8 years  parrello  New script to list expression-data genomes.
svr_evidence.pl  1.1  9 years  disz  New svr script to get evidence code
svr_dna_seq.pl  1.2  9 years  parrello  More server script stuff.
svr_distinct_otus.pl  1.4  9 years  parrello  Added support for specifying input IDs on the command line.
svr_discriminating_functions.pl  1.3  9 years  parrello  Discrimination functions support scripts.
svr_determine_sets_of_related_contigs.pl  1.4  9 years  parrello  Documentation fixes.
svr_delete_RAST_job.pl  1.3  10 years  olson  Fix 666666 problem. Add support for using the test server.
svr_cut_domain.pl  1.1  9 years  overbeek  cut domains from sequences
svr_coupled_reactions.pl  1.1  8 years  parrello  New chemistry-based scripts.
svr_corresponding_genes2.pl  1.1  9 years  olson  New corresponding genes computer.
svr_corresponding_genes.pl  1.24  9 years  overbeek  fix command line arguments
svr_corr_by_exp.pl  1.5  8 years  parrello  Changed to batch the input instead of slurping it.
svr_coregulated_by_correspondence.pl  1.6  8 years  overbeek  handle peg related to peg
svr_copy_to_RAST_dir.pl  1.3  9 years  olson  fix
svr_contigs_in_genome.pl  1.3  9 years  parrello  Added support for specifying input IDs on the command line.
svr_compare_feature_tables.pl  1.7  9 years  gdpusch  Fixed typo in variable-name
svr_column_of_subsystem.pl  1.1  9 years  olson  server script to pull a subsystem colum
svr_cohesion_groups.pl  1.3  8 years  fangfang  add more options
svr_co_occurrence_evidence.pl  1.4  9 years  disz  FigFam 6 digit problem
svr_cluster_pegs.pl  1.1  9 years  overbeek  two small utilities
svr_closest_genes.pl  1.1  9 years  parrello  More server script stuff.
svr_close_genomes.pl  1.1  9 years  parrello  More server script stuff. Thought I'd already installed these last week...
svr_call_rnas.pl  1.1  9 years  parrello  More server scripts.
svr_call_pegs.pl  1.2  9 years  overbeek  fix POD stuff
svr_by_taxonomy.pl  1.3  9 years  overbeek  fix parameter passing
svr_blast.pl  1.1  8 years  overbeek  interface to blast
svr_big_repeats.pl  1.1  9 years  overbeek  tool to search for large repeats
svr_atomic_regulons.pl  1.1  8 years  parrello  Added to allow retrieval of pegs in atomic regulons.
svr_assign_using_figfams.pl  1.11  8 years  gdpusch  Fixed "die" statement that lacks any conditional.
svr_assign_to_dna_using_figfams.pl  1.15  9 years  overbeek  default kmer=8
svr_all_subsystems.pl  1.9  9 years  parrello  Fixed POD errors. Added examples.
svr_all_reactions.pl  1.1  8 years  parrello  New chemistry-based scripts.
svr_all_models.pl  1.2  8 years  overbeek  keep only Seed models
svr_all_genomes.pl  1.2  9 years  parrello  First round of script updates & additions for tutorial.
svr_all_figfams.pl  1.2  9 years  parrello  Documentation fixes.
svr_all_features.pl  1.6  9 years  fangfang  Added svr_all_genomes, and modified svr_all_features to make it take genome IDs ...
svr_all_experiments.pl  1.1  8 years  parrello  Added to get experiments for each genome.
svr_align_using_muscle.pl  1.2  9 years  gdpusch  Fixed incorrect function names.
svr_align_seqs.pl  1.13  8 years  fangfang  add multithread support for mafft
svr_aliases_to_pegs.pl  1.1  9 years  parrello  New script for Ross
svr_aliases_of.pl  1.6  8 years  disz  Added precise option
svr_ali_to_html.pl  1.2  8 years  fangfang  added SAS header
svr_add_lengths_to_blast.pl  1.1  8 years  overbeek   simple utility to add sequence lengths to m8 blast output
svr_ach_lookup.pl  1.10  9 years  parrello  More server script stuff. Thought I'd already installed these last week...
svr_SAP.t  1.4  9 years  olson  update tests
svr_NCBI_taxonomy.pl  1.2  8 years  golsen  Add more formats in which abbreviated lineages can be returned. Add long form of...
svr_ACH.t  1.1  10 years  olson  new tests
svr.pl  1.2  9 years  olson  add . to include path
summarize_taxonomy_by_blast.pl  1.9  11 years  redwards  removing fatal error if 0 or 1 hits
subtree_of.pl  1.2  14 years  olson  Add license words.
subsys_info.pl  1.1  11 years  overbeek  subsys_info is subsystem information for Verionika
subsys2pubmed.pl  1.4  12 years  hwang  change script to add new attribute after each subsystem versus after all subsyst...
submit_to_iprscan_on_biocluster.pl  1.1  12 years  mkubal  run iprscan on cluster
submit_genome_to_signalP.pl  1.2  12 years  mkubal  test for dir exist
submit_genome_to_rpsblast_against_CDD_on_biocluster.pl  1.2  12 years  mkubal  test for dir exist
submit_ff_test.pl  1.6  10 years  arodri7  commit changes
stop_services.pl  1.5  14 years  olson  Add license words.
start_services.pl  1.12  14 years  olson  Add license words.
start_dbserver.pl  1.2  14 years  olson  Add license words.
start_data_for_set_of_pegs.pl  1.6  12 years  gdpusch  Added FIGV support. -- /gdp
sprout_search.pl  1.2  14 years  olson  Add license words.
splitup.pl  1.4  14 years  olson  Add license words.
split_sims.pl  1.3  14 years  olson  Add license words.
split_sequences_into_sets.pl  1.5  10 years  overbeek  handle asym connections
split_clean_unclean_families.pl  1.4  13 years  overbeek  fixes for splitting families into clean/unclean
split_by_genome.pl  1.1  13 years  overbeek  split_by_genome can be used to split a score or BBH file
split_assignments_based_on_subsystems.pl  1.1  13 years  overbeek  next version of the STAG code
split_and_trim_sequences.pl  1.14  12 years  overbeek  fix problem when repeats occur
split_and_install_pchs.pl  1.2  14 years  olson  Add license words.
sphinx_index_genome.pl  1.7  8 years  olson  More fixups.
sp2fasta.pl  1.2  14 years  olson  Add license words.
sort_and_split_bbhs.pl  1.5  12 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
sketch_tree.pl  1.3  9 years  golsen  Many changes and updates.
sims_between.pl  1.7  12 years  overbeek  updates on close connections
sims_all.pl  1.6  10 years  overbeek  remove paralogs before computing conections
similar_to.pl  1.4  14 years  olson  Add license words.
show_structured_english.pl  1.1  11 years  disz  Ross's code to generate annotations for NCBI
show_reconfig_cmd.pl  1.3  14 years  olson  Add license words.
set_to_relation.pl  1.2  14 years  olson  Add license words.
set_not_private.pl  1.1  11 years  bartels  *** empty log message ***
server_paper_figure2.pl  1.2  9 years  parrello  Removed genetic codes so program fits better on a page.
server_paper_example7.pl  1.4  9 years  chenry  Corrected a few bugs in the example script.
server_paper_example6.pl  1.3  9 years  parrello  Fixed for server paper.
server_paper_example5.pl  1.3  9 years  disz  Switched to ANNO server
server_paper_example4.pl  1.3  9 years  parrello  Fixed to use the correct servers.
server_paper_example3.pl  1.5  10 years  disz  converted to new SAP server
server_paper_example2.pl  1.7  9 years  disz  Changed to use ANNO server
server_paper_example1.pl  1.12  9 years  parrello  Documentation fix for server paper.
sequence_length_histogram.pl  1.6  9 years  olson  Include in SAS
sequence_dereplication.pl  1.1  10 years  arodri7  first version of sequence_dereplication. Script takes sequences which are subset...
select_genomes_for_sprout.pl  1.2  14 years  olson  Add license words.
seed_run_task.pl  1.2  13 years  olson  readonly fixes; seed-run-job update to run from input file
seed_run_job.pl  1.4  13 years  olson  readonly fixes; seed-run-job update to run from input file
seed_job_scheduler.pl  1.3  14 years  olson  Add license words.
seed2tbl.pl  1.3  9 years  disz  FigFam 6 digit problem
seed2pir.pl  1.3  13 years  overbeek  RAE: moving PIRSF to links
seed2gff.pl  1.36  11 years  redwards  getting rid of need for strain info
seed2genbank.pl  1.5  9 years  redwards  fixing major bug that was removing all stop positions
score_ifcs_mcauliffe.pl  1.2  13 years  overbeek  RAE: correcting indirect functional coupling score
score_ifcs.pl  1.4  13 years  overbeek  RAE: More direct and indirect functional coupling scores
score_dfcs_mcauliffe.pl  1.5  13 years  overbeek  limit decimal positions in score
score_dfcs.pl  1.3  13 years  overbeek  RAE: removing the header that should not be in the source
same_subsys.pl  1.1  13 years  overbeek  fixes to extract_genomes
same_figfam.pl  1.2  12 years  overbeek  handle bad input in same_figfam
salvage_subsystem_rows.pl  1.6  13 years  overbeek  fixes to salvage code
salvage_master_annotations.pl  1.3  13 years  overbeek  fixes to salvage code
salvage_annotations.pl  1.6  13 years  olson  bugfix.
runclustalw.pl  1.4  12 years  overbeek  add computation of alignments to building FIGFAMS
run_start_predictions_for_spreadsheet.pl  1.6  14 years  olson  Add license words.
run_start_predictions_for_all_subsystems.pl  1.4  14 years  olson  Add license words.
run_scenarios.pl  1.5  11 years  dejongh  switch to scenario_directory
run_remote_Phobius_for_genomes.pl  1.1  12 years  mkubal  run for all complete prok genomes
run_remote_Phobius_for_genome_for_RAST.pl  1.1  12 years  mkubal  for use with RAST server
run_remote_Phobius_for_genome.pl  1.1  12 years  mkubal  for single genome
run_remote_Phobius_for_fasta.pl  1.1  11 years  mkubal  fasta file as input
run_remote_PHOBIOUS.pl  1.1  12 years  mkubal  runs Phobius computation for given geneome
run_peg_job_worker.pl  1.4  14 years  olson  Add license words.
run_muscle.pl  1.3  8 years  golsen  Update libraries used.
run_model_generation_v3.pl  1.3  11 years  dejongh  switch to scenario_directory
run_model_generation_all.pl  1.1  12 years  formsma  This script will generate models for all complete genomes in the seed. - Kevin
run_model_generation.pl  1.17  11 years  dejongh  switch to scenario_directory
run_glimmer3.pl  1.14  9 years  parrello  Added "-verbose" option so tracing can be turned on from the servers.
run_glimmer2.pl  1.7  12 years  gdpusch  Added support for multiple genetic codes. -- /gdp
run_gene_calling_scripts.pl  1.3  10 years  overbeek  fix first arg on call to mark_picked_genes
run_flux_optimization.pl  1.4  11 years  dejongh  switch to scenario_directory
run_find_subsys_against_all_genomes.pl  1.2  12 years  overbeek  updates to computation of VCs
run_fc.pl  1.2  14 years  olson  Add license words.
run_HMM_search_on_timelogic.pl  1.1  12 years  mkubal  version 1.0
root_at.pl  1.2  14 years  olson  Add license words.
roles_in_subsystem.pl  1.2  14 years  olson  Add license words.
restrict_to_genomes.pl  1.3  14 years  olson  Add license words.
restrict_by_similarity.pl  1.4  14 years  olson  Add license words.
restore_translation_rules.pl  1.2  14 years  olson  Add license words.
restore_assignments.pl  1.2  14 years  olson  Add license words.
restore_annotations.pl  1.2  14 years  olson  Add license words.
reps_and_close.pl  1.2  12 years  overbeek  add make_trimmed_alignment_from_ids
representative_tree.pl  1.2  14 years  olson  Add license words.
representative_sequences.pl  1.6  9 years  overbeek  keep representative_sequences, but make it a shadow of the new svr_representativ...
report_changes.pl  1.2  14 years  olson  Add license words.
rep_sets.pl  1.1  10 years  disz  Old code finally checked in to create representative sets
rep_genomes.pl  1.1  13 years  overbeek  fixes to representative tree generation and added rep_genomes
renumber_seed_dir.pl  1.4  9 years  olson  Don't fail if Features dir does not exist.
renumber_features.pl  1.13  9 years  gdpusch  Modified a debugging statement.
remove_sims_not_in_nr.pl  1.1  12 years  olson  Missing scripts.
remove_rna_overlaps.pl  1.10  11 years  gdpusch  Added setting of VERBOSE from metafile. -- /gdp
remove_multiple_occurring_probes.pl  1.1  9 years  overbeek  remove multiple occurring probes
remove_embedded_pegs.pl  1.19  9 years  gdpusch  Modified to use Kmers.
remove_clustered_pchs3.pl  1.1  12 years  olson  Missing scripts.
remove_clustered_pchs2.pl  1.1  12 years  olson  Missing scripts.
remove_clustered_pchs.pl  1.10  13 years  overbeek  fix rfemove_clustered_PCHs to count correctly
relevant_pchsG.pl  1.4  14 years  olson  Add license words.
relevant_PCHs.pl  1.3  14 years  olson  Add license words.
relabel_nodes.pl  1.2  14 years  olson  Add license words.
rel2tabs.pl  1.1  13 years  overbeek  minor tools
register_genome_with_clearinghouse.pl  1.1  12 years  olson  Missing scripts.
register_features_with_clearinghouse.pl  1.2  14 years  olson  Add license words.
register_features_batch.pl  1.2  14 years  olson  Add license words.
reformat_timelogic_sims.pl  1.2  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_fasta.pl  1.2  14 years  olson  Add license words.
reformat_dsim_dbs.pl  1.2  14 years  olson  Add license words.
reformat_contigs.pl  1.24  9 years  gdpusch  Fixed contig-ID "0" bug
reformat_circular_contigs.pl  1.1  10 years  arodri7  added reformat_circular_contigs for rapid_propagation_plasmids
reduce_sims.pl  1.12  10 years  olson  fix nasty little bug that drops sims
recompute_comparison.pl  1.1  11 years  bartels  *** empty log message ***
rebuild_global_chromosomal_clusters.pl  1.2  12 years  overbeek  version of rebuild_global_chromosomal_clusters that works
read_write_excel.pl  1.1  13 years  overbeek  RAE: Initial release of a simple script to read and write excel files to allow e...
rationalize_blast.pl  1.3  14 years  olson  Add license words.
rapid_subsystem_inference.pl  1.17  9 years  redwards  removing zero length keys
rapid_propagation_plasmid.pl  1.22  9 years  disz  FigFam 6 digit problem
rapid_propagation4.pl  1.7  8 years  gdpusch  Fixed problem with virus/plasmid branch in "keep_genecalls" mode.
rapid_propagation3.pl  1.10  9 years  olson  Support family determiantion.
rapid_propagation2.pl  1.5  9 years  gdpusch  Minor cosmetic changes.
rapid_propagation.pl  1.75  10 years  olson  use $num_neighbors internally instead of hardwired constant
questionable_calls.pl  1.2  14 years  olson  Add license words.
put_directory_in_one_file.pl  1.2  14 years  olson  Add license words.
purge_tbl.pl  1.1  13 years  overbeek  Removes duplicate entries from tbl file. -- /gdp
purge_fasta.pl  1.1  13 years  overbeek  Removes duplicate entries from fasta file. -- /gdp
pull_sp_entries.pl  1.2  14 years  olson  Add license words.
pull_orfs.pl  1.7  9 years  gdpusch  Corrected regexp error.
pull_fasta_entries.pl  1.8  10 years  olson  do not attempt to remap incoming ids
pubmed_gene2peg.pl  1.2  13 years  redwards  making sure gene id is right
pubbed_fids.pl  1.1  10 years  parrello  New script to find features with publications attached.
propagate_subsys_changes_to_figfams.pl  1.12  10 years  arodri7  commit changes
promote_orfs_to_pegs.pl  1.15  9 years  gdpusch  Code restructured, and modified to fail gracefully if there are no closest genom...
project.pl  1.2  14 years  olson  Add license words.
process_sim_deletions_and_replacements.pl  1.3  14 years  olson  Add license words.
process_one_exp_dir.pl  1.3  8 years  olson  Support for peg.id.corr genomes like 272843.1
process_new_sims.pl  1.6  12 years  olson  Rollup of various rast-related changes.
prepare_metagenome_files_for_ftp.pl  1.3  11 years  mkubal  checks for PUBLIC file
prepare_metagenome_files_for_download.pl  1.4  11 years  mkubal  full loop
prep_viz.pl  1.2  14 years  olson  Add license words.
predicted_vs_actual.pl  1.1  10 years  overbeek  basic metagenomic tools
predict_starts.pl  1.8  12 years  gdpusch  Added FIGV support. -- /gdp
predict_scenarios.pl  1.2  12 years  formsma  Added code to automatically run 'run_scenarios All' if it hasn't been run. These...
pp.pl  1.3  14 years  olson  Add license words.
potentially_missed_assignments.pl  1.1  13 years  overbeek  add potentially_missed_assignments
potentially_cotranscribed.pl  1.2  14 years  olson  Add license words.
postprocess_computed_sims.pl  1.2  14 years  olson  Add license words.
possibly_truncated.pl  1.2  14 years  olson  Add license words.
possible_frameshifts.pl  1.1  12 years  overbeek  update possible_frameshifts
pop_vec.pl  1.1  10 years  overbeek  code for processing fabrics and population estimates
pick_feature_set.pl  1.1  10 years  overbeek  choose genes from candidates
pegs_in_subsystems.pl  1.8  10 years  overbeek  fix documentation
pegs_in_subsystem.pl  1.6  10 years  overbeek  check for aux roles
pegs_in_conflict.pl  1.3  14 years  olson  Add license words.
pegs.pl  1.3  14 years  olson  Add license words.
peg_to_subsystems.pl  1.3  14 years  olson  Add license words.
peg_to_pdb.py  1.2  14 years  olson  Add license words.
peg_to_name.pl  1.4  14 years  olson  Add license words.
peg2pubmed.pl  1.1  13 years  hwang  Added two scripts that will generate pubmed files
partition_prots.pl  1.4  10 years  overbeek  check to make sure sims are working
parse_uniparc.pl  1.1  12 years  mkubal  v1
parse_mart.py  1.6  14 years  olson  Add license words.
parse_genbank.pl  1.33  8 years  gdpusch  Added "-user_trans_only" flag.
paint_tree.pl  1.3  14 years  olson  Add license words.
package_translation_rules.pl  1.2  14 years  olson  Add license words.
package_subsystems.pl  1.5  13 years  overbeek  fixes to deleted_features, replace_features_with, etc
package_sims.pl  1.2  14 years  olson  Add license words.
package_raw_data_for_transplant.pl  1.2  14 years  olson  Add license words.
package_lightweight_code.pl  1.2  14 years  olson  Add license words.
package_code.pl  1.2  14 years  olson  Add license words.
package_assignments.pl  1.8  14 years  olson  Add license words.
package_annotations.pl  1.9  14 years  olson  Add license words.
p2p_sync_from_remote.pl  1.4  14 years  olson  Add license words.
p2p_sync_cron.pl  1.3  14 years  olson  Add license words.
p2p_daemon.pl  1.2  14 years  olson  Add license words.
order_sets.pl  1.3  14 years  olson  Add license words.
order_seqs_on_length.pl  1.1  12 years  overbeek  add utilities for computing alignments
order_figfams.pl  1.1  13 years  overbeek  order_figfams
order_corrections_for_start_predictions.pl  1.5  12 years  gdpusch  Added FIGV support. -- /gdp
nmpdr2gff.pl  1.1  13 years  overbeek  RAE: Changes to gff3 files for NMPDR and adding nmpdr2gff for creating the files...
new_versions_of_features.pl  1.1  13 years  overbeek  add new_versions_of_features
myjoin.pl  1.1  13 years  overbeek  fix building FigFamData
modify_tree.pl  1.1  9 years  golsen  A general purpose tree modification utility.
mg_user_id_to_unique.pl  1.2  11 years  mkubal  full loop
metagenome2genbank.pl  1.4  11 years  mkubal  includes data from meta.xml
meta.pl  1.12  10 years  jared  added update_path
merge_translation_rules.pl  1.7  14 years  olson  Add license words.
merge_missing_gene_output.pl  1.3  9 years  olson  bugfix
merge_gene_sets.pl  1.1  9 years  overbeek  code from Hope
merge_families.pl  1.3  12 years  overbeek  add strip comments argument on function_of
merge_assignments.pl  1.1  10 years  bartels  *** empty log message ***
merge_annotations.pl  1.3  14 years  olson  Add license words.
md5.c  1.3  14 years  olson  Doh, put proper comments in for C code.
match_dna_to_aligned_prots.pl  1.4  14 years  olson  Add license words.
mark_picked_genes.pl  1.2  10 years  overbeek  fix order of arguments
mark_nr.pl  1.2  14 years  olson  Add license words.
mark_genome_as_phage.pl  1.1  8 years  redwards  two phage specific scripts
map_to_scaffold.pl  1.4  11 years  olson  Actually write out the changed entries.
map_sims_for_bigfc.pl  1.2  14 years  olson  Add license words.
map_sims.pl  1.5  14 years  olson  Add license words.
map_pegs.pl  1.3  13 years  parrello  Fixed obsolete form of boundaries_of.
map-nr-ids-to-ncbi-std.pl  1.1  11 years  olson  Script to map IDs in a SEED NR into forms acceptable to the indexed NCBI fasta p...
make_uniprot_corr.pl  1.2  11 years  overbeek  build uniprot correspondence
make_trimmed_alignment_from_ids.pl  1.13  11 years  overbeek  return empty list of failure to open FIFfam
make_transferable_tarfiles.pl  1.3  14 years  olson  Add license words.
make_transferable_chunks.pl  1.4  14 years  olson  Add license words.
make_timestamps.pl  1.4  13 years  overbeek  add initial version of FIGO.pm - OO services
make_tf_equivalog_file.pl  1.1  11 years  bartels  *** empty log message ***
make_subsystems_from_clusters.pl  1.5  14 years  olson  Add license words.
make_subsys_based_families2.pl  1.1  10 years  arodri7  commit changes
make_subsys_based_families.pl  1.14  11 years  overbeek  do not use genomes with variants beginning with an asterisk in forming FIGfams b...
make_sprout_upstream.pl  1.2  14 years  olson  Add license words.
make_sprout_bbhs.pl  1.2  14 years  olson  Add license words.
make_spreadsheet_and_notes.pl  1.3  14 years  olson  Add license words.
make_sp_uni_files.pl  1.4  12 years  wilke  changed check for input and output directory the directories may exists, so don'...
make_sp_org_table.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_func_syn_dicts.pl  1.2  14 years  olson  Add license words.
make_sp_desc_with_org.pl  1.2  14 years  olson  Add license words.
make_sims_and_fc_data.pl  1.1  10 years  overbeek  add wrapper to building partition-based similarity and fc data
make_sim_tab.pl  1.8  12 years  olson  compute_pchs_from_sims.pl
make_sim_sets.pl  1.3  14 years  olson  Add license words.
make_sim_part_data.pl  1.1  10 years  overbeek  add command to build similarity partitions
make_scored_instances.pl  1.4  10 years  overbeek  minor changes
make_reduce_sims_index.pl  1.1  12 years  olson  new script
make_rates.pl  1.2  14 years  olson  Add license words.
make_protein_weights_and_rates.pl  1.2  12 years  golsen  Moving some tree building tools into packages.
make_protein_sets.pl  1.4  14 years  olson  Add license words.
make_prosite_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_proposed_assignments_for_consistency.pl  1.4  13 years  overbeek  fixes to wseekly statistics
make_proml_tree_0.pl  1.1  12 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
make_proml_tree.pl  1.6  12 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
make_probes_to_genes.pl  1.8  8 years  dejongh  check for same contig when matching probe to peg
make_pir_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_phob_from_seqs.pl  1.7  14 years  olson  Add license words.
make_phob_from_ids.pl  1.3  14 years  olson  Add license words.
make_pfam_ontology.pl  1.4  11 years  mkubal  provides usage when no argument given
make_peg_maps_from_fasta.pl  1.2  10 years  olson  need to compute sims both directions because connections_between now uses bbhs.
make_peg_maps.pl  1.3  14 years  overbeek  minor fixes
make_peg_map_from_tbl.pl  1.3  10 years  olson  fix bug that made empty output
make_pdb_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_partition_reps_worker.pl  1.3  10 years  arodri7  commit change
make_partition_repsW.pl  1.1  10 years  overbeek  try
make_partition_repsP.pl  1.4  10 years  arodri7  commit change
make_partition_reps.pl  1.1  10 years  overbeek  try
make_parallel_proml_run.pl  1.2  12 years  overbeek  add rates to phylogeny stuff
make_overlap_report.pl  1.21  9 years  gdpusch  Fixed major bug handling negative strand; also minor cosmetic changes for readab...
make_occ_counts.pl  1.2  14 years  olson  Add license words.
make_neigh_joining_tree.pl  1.8  12 years  overbeek  debugged version of bring_tree_up_to_ali
make_ncbi_files.pl  1.4  12 years  wilke  changed check for existing directories
make_model_spreadsheets.pl  1.2  11 years  dejongh  switch to scenario_directory
make_md5_figfams_file.pl  1.1  11 years  arodri7  script makes the md5 to figfams file
make_match_table.pl  1.2  14 years  olson  Add license words.
make_maps_from_sub.py  1.5  14 years  olson  Add license words.
make_ma_html.pl  1.2  8 years  overbeek  minor fixes
make_kegg_files.pl  1.5  12 years  overbeek  Update parsing of NAME field to reflect change in source file. -- /gdp
make_jpg.pl  1.2  14 years  olson  Add license words.
make_interpro_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_initial_partition_scores.pl  1.1  10 years  overbeek  additions to support partitioning of sims
make_indexes.pl  1.17  9 years  dejongh  Fix KEGG location
make_go_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_genome_dir_for_close.pl  1.9  11 years  gdpusch  Fixed handling of spliced loci. -- /gdp
make_figfams.pl  1.3  13 years  overbeek  families.2c should get current function - not family function
make_figfam_tree_worker.pl  1.2  9 years  disz  FigFam 6 digit problem
make_figfam_tree.pl  1.2  9 years  disz  FigFam 6 digit problem
make_fig_files.pl  1.3  14 years  olson  Add license words.
make_fasta_btree.pl  1.1  12 years  olson  Utility for creating btree access for fasta files.
make_fam_tabs.pl  1.5  13 years  overbeek  RAE: Protein Families interface and construction
make_external_sequence_data.pl  1.2  13 years  olson  remove .pl from invocations
make_coreg_conjectures_based_on_subsys.pl  1.4  8 years  olson  Update to expression pipeline code
make_close_strain_family_tabs.pl  1.2  13 years  overbeek  fixes to wseekly statistics
make_close_strain_data.pl  1.14  10 years  overbeek  fixes to making close strain data
make_close.pl  1.7  13 years  parrello  Fixed obsolete form of boundaries_of.
make_cdd_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_calls_for_start_predictions.pl  1.4  12 years  gdpusch  Added FIGV support. -- /gdp
make_calls.pl  1.4  14 years  olson  Add license words.
make_binary.pl  1.2  14 years  olson  Add license words.
make_attribute_index.pl  1.6  14 years  olson  Add license words.
make_assignments_set.pl  1.3  14 years  olson  Add license words.
make_assignments_fit_initial_css.pl  1.4  14 years  olson  Add license words.
make_assertions_from_uploads.pl  1.3  11 years  overbeek  get rid of debugging message
make_annotations_for_sprout.pl  1.12  14 years  olson  Add license words.
make_SignalP_attributes.pl  1.2  12 years  mkubal  changed ; to :: for key separator
make_SBML_model.pl  1.6  11 years  dejongh  switch to scenario_directory
make_Phobius_attributes.pl  1.2  12 years  mkubal  added date as 2nd argument
make_PROSITE_PIR_PRODOM_attributes.pl  1.3  12 years  mkubal  fix to score format
make_PHOBs_for_subsystems.pl  1.5  14 years  olson  Add license words.
make_PFAM_HMM_derived_attributes.pl  1.2  12 years  mkubal  added date as 2nd argument
make_PDB_attributes.pl  1.2  12 years  mkubal  fix to score format
make_Ontology_database.pl  1.3  11 years  mkubal  provides usage when no argument given
make_MPS_model_v2.pl  1.2  11 years  dejongh  switch to scenario_directory
make_MPS_model.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_IPR_PFAM_GO_attributes.pl  1.3  12 years  mkubal  fix to score format
make_FigFamsData.pl  1.4  13 years  overbeek  order generated FIGfams
make_CELLO_and_TMPRED_attributes.pl  1.2  12 years  mkubal  changed ; to :: for key separator
make_CDD_attributes.pl  1.2  12 years  mkubal  fix to score format
maint-remove-obsolete-aliases.pl  1.1  12 years  olson  Missing scripts.
macapp_files_to_genome_dir.pl  1.2  9 years  olson  Banish cp.
ma_pipeline_shewanella.pl  1.6  9 years  overbeek  fixes to pipeline
ma_pipeline_ecoli.pl  1.2  9 years  overbeek  pipeline for Ecoli
ma_pipeline.pl  1.15  9 years  overbeek  get rid of RMA Key
ma.cgi  1.1  9 years  overbeek  added massaging and voting
location_of.pl  1.2  14 years  olson  Add license words.
load_wikipedia.pl  1.1  10 years  olson  Wikipedia cache loader.
load_ss_classification.pl  1.1  11 years  redwards  adding ss classification methods
load_sims.pl  1.10  13 years  olson  If we are loading unmapped files (as generated by make_close -no-map and make_s...
load_sets.pl  1.5  14 years  olson  Add license words.
load_protein_families.pl  1.9  14 years  overbeek  RAE: extending protein families
load_pirsf.pl  1.14  13 years  overbeek  RAE: correcting load_pirsf not recognizing a firewall
load_peg_mapping.pl  1.12  8 years  olson  Caching / FCGI speedup modifications.
load_pch_pins.pl  1.2  14 years  olson  Add license words.
load_locks.pl  1.1  13 years  overbeek  introduce locks on features to block assignments
load_local_maps.pl  1.3  14 years  olson  Add license words.
load_literature.pl  1.3  14 years  olson  Add license words.
load_links.pl  1.7  11 years  olson  Only load links from files ending in "links" (rather than files with it anywhere...
load_kegg.pl  1.15  9 years  dejongh  Fix KEGG location
load_id_correspondence.pl  1.3  11 years  olson  updates to the load_id_correspondence loader and searching code.
load_hugo.pl  1.6  14 years  olson  Add license words.
load_go.pl  1.2  13 years  overbeek  put in the fr2go stuff
load_features.pl  1.24  11 years  olson  fix tmp file name.
load_external_orgs.pl  1.3  14 years  olson  Add license words.
load_ec_names.pl  1.6  10 years  olson  support for change in format to the KEGG/ECtable.
load_dlits.pl  1.5  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
load_distances.pl  1.5  14 years  olson  Add license words.
load_coupling_btree.pl  1.1  13 years  olson  BTREE-index versions of these. Experimental still.
load_coupling.pl  1.9  13 years  olson  Remove debugging.
load_close.pl  1.9  12 years  overbeek  tighten length constraints for figfam matching
load_chromosomal_clusters.pl  1.2  14 years  olson  Add license words.
load_bbhs_btree.pl  1.1  13 years  olson  BTREE-index versions of these. Experimental still.
load_bbhs.pl  1.15  11 years  olson  *** empty log message ***
load_attributes.pl  1.46  8 years  redwards  changing the attribute of the genome table
load_atomic_regulons.pl  1.1  8 years  olson  initial atomic regulon table loader
load_abstract_coupling.pl  1.3  13 years  parrello  Changed to use a single-character delimiter (for compatability with PostGRES).
load_ACH_resolution_DB.pl  1.4  11 years  overbeek  fixes to quotemeta characters in loading comments
list_genomes.pl  1.2  14 years  olson  Add license words.
lengths_of_contigs.pl  1.2  14 years  olson  Add license words.
keep_only.pl  1.2  14 years  olson  Add license words.
jgi_data_merge.pl  1.2  8 years  golsen  Fix the taxonomy to use NCBI full taxonomy if TAXONOMY does not exist.
is_prokaryotic.pl  1.2  14 years  olson  Add license words.
is_eukaryotic.pl  1.2  14 years  olson  Add license words.
is_bacterial.pl  1.2  14 years  olson  Add license words.
is_archaeal.pl  1.2  14 years  olson  Add license words.
interval.pl  1.2  14 years  olson  Add license words.
install_translation_rules.pl  1.3  14 years  olson  Add license words.
install_subsystems.pl  1.2  14 years  olson  Add license words.
install_rast_batch.pl  1.4  12 years  olson  more fixes
install_partitions.pl  1.5  9 years  disz  FigFam 6 digit problem
install_partition_reps.pl  1.2  10 years  arodri7  commit change
install_new_coupling_data.pl  1.3  12 years  olson  add option to install from a jobdir
install_lightweight_code.pl  1.2  14 years  olson  Add license words.
install_features_batch.pl  1.1  11 years  olson  Add new script to install a batch of genomid.tbl / genomeid.fasta files. Initial...
install_feature_updates.pl  1.2  14 years  olson  Add license words.
install_code.pl  1.2  14 years  olson  Add license words.
install_assignments.pl  1.7  14 years  olson  Add license words.
install_anticipated_functions.pl  1.3  11 years  olson  Introduct &FIG::get_figfams_data()
install_annotations.pl  1.4  14 years  olson  Add license words.
install-data.pl  1.8  12 years  olson  fix to dvd data installer
insert_prot_into_tree.pl  1.14  12 years  golsen  Continuing the update of tree packages and programs
insert_into_a_tree.pl  1.5  12 years  overbeek  add tree_neighbors and latest phylogeny stuff
insert_all.pl  1.2  14 years  olson  Add license words.
insert.pl  1.2  14 years  olson  Add license words.
initialize_figfams.pl  1.12  9 years  disz  FigFam 6 digit problem
initialize_ann_and_ev.pl  1.3  11 years  olson  undo bogus commit
initialize_alignments_for_subsystems.pl  1.2  13 years  overbeek  fixes to extract_genomes, salvage_subsystem_rows and initialize_alignments_for_s...
initial_set.pl  1.2  14 years  olson  Add license words.
init_peg_job_scheduler.pl  1.4  14 years  olson  Add license words.
init_maps.pl  1.3  14 years  olson  Add license words.
init_dbserver.pl  1.3  14 years  olson  Add license words.
init_FIG.pl  1.12  9 years  olson  fix typo
indirect_functional_coupling_mcauliffe.pl  1.5  13 years  overbeek  indirect functional coupling should not be from a PEG to itself
indirect_functional_coupling.pl  1.5  13 years  overbeek  indirect functional coupling should not be from a PEG to itself
index_translations_MD5.pl  1.4  10 years  olson  revert changes
index_translations.pl  1.24  9 years  olson  Add index on fileno.
index_translation_files.c  1.8  8 years  redwards  ignoring stops
index_subsystems.pl  1.13  8 years  olson  fix ss indexing
index_sprout.pl  1.12  14 years  olson  Add license words.
index_sims_file.c  1.7  10 years  golsen  Bob added an #include <sys/types.h>. This is committing that code change.
index_sims.pl  1.12  10 years  olson  Bump id size.
index_pins.pl  1.3  13 years  olson  new pin indexer
index_nr.pl  1.2  12 years  olson  compute length btree also
index_neighborhoods.pl  1.3  14 years  olson  Add license words.
index_figv_annos.pl  1.1  11 years  olson  Index scripts for FIGV accleration.
index_feature_dir_fasta.pl  1.1  11 years  olson  Index scripts for FIGV accleration.
index_fasta.pl  1.2  14 years  olson  Add license words.
index_contigs.pl  1.12  8 years  redwards  not reopening a file twice!
index_contig_files.c  1.5  13 years  olson  fix to work on 64-bit linux
index_annotations.pl  1.11  12 years  olson  bugfix
index_anno_clearinghouse.pl  1.3  12 years  olson  multiple id support, build fixes
index-pegsyn2.pl  1.1  11 years  olson  new version of pegsyn indexer that presorts data before inserting into the btree...
index-pegsyn.pl  1.1  12 years  olson  Missing scripts.
import_subsystems.pl  1.22  14 years  olson  Add license words.
import_similarity_bundle.pl  1.3  11 years  parrello  Fixed a POD error.
import_external_sequences_step3.pl  1.5  14 years  olson  Add license words.
import_external_sequences_step1.pl  1.8  14 years  olson  Add license words.
iedb.pl  1.10  13 years  overbeek  RAE: bugger, correcting the array dereferencing
identify_organism.pl  1.2  10 years  olson  changes for new server stuff
html_parser.py  1.2  14 years  olson  Add license words.
glue_tbl_to_metabolic_reconstruction.pl  1.1  10 years  olson  more anno server fixes, add some missing files
gi2fig.pl  1.3  14 years  olson  Add license words.
gff_statistics.pl  1.1  13 years  redwards  releasing gff statistics
gff2tab.pl  1.5  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
gff2seed.pl  1.29  10 years  redwards  removing check for refseq ids
gff2ncbitab.pl  1.3  11 years  olson  add swissprot
gff2Ontology.pl  1.4  14 years  olson  Add license words.
get_translations.pl  1.3  13 years  overbeek  get_translations can take PEG ids from STDIN
get_taxid_journals.pl  1.1  12 years  hwang  get journals from PMC using taxide
get_synonyms_from_ach_for_id.pl  1.2  11 years  wilke  *** empty log message ***
get_subsystem_properties.pl  1.1  12 years  overbeek  minor modifications to get subsystems statistics
get_ss_connections.pl  1.12  10 years  redwards  only call if not in a ss
get_sims_for_start_predictions.pl  1.5  12 years  gdpusch  Added FIGV support. -- /gdp
get_rna_features_for_calling_genes.pl  1.2  10 years  overbeek  get rid of proteins
get_pubmed_journals.pl  1.5  12 years  hwang  update comment that this is for peg curation
get_potential_starts_for_start_predictions.pl  1.3  12 years  gdpusch  Added FIGV support. -- /gdp
get_pathways_for_EC.pl  1.2  14 years  olson  Add license words.
get_pairs.pl  1.1  10 years  parrello  New script to find certain functional roles close together.
get_nr_entries_without_sims.pl  1.4  14 years  olson  Add license words.
get_neighbors_and_corr_to_ref.pl  1.7  9 years  olson  remove cat and shell usage.
get_long_enough.pl  1.2  14 years  olson  Add license words.
get_journals_for_org.pl  1.1  12 years  hwang  this script is the backend to get journals using taxonomy id or name. This calls...
get_journals_for_frole.pl  1.1  12 years  hwang  Files to get journal information from PubMed
get_id_mapping_for_list_of_IDs.pl  1.1  11 years  wilke  Draft version for id mapping
get_genomes_from_ncbi.pl  1.1  10 years  wilke  *** empty log message ***
get_figfam_funcs.pl  1.1  13 years  overbeek  add install_anticipated_functions and some FIGfam tracking stuff
get_fasta_for_tbl_entries.pl  1.11  10 years  gdpusch  Modified to remove complaints about uninitialed values when TBL entry does not c...
get_evaluation_check_rast_new_vs_old.pl  1.1  12 years  bartels   compare old rast with development version
get_evaluation_check.pl  1.3  12 years  bartels  added option -a for showing pegs that do not match via blast
get_ev_codes.pl  1.15  11 years  parrello  Updated comments to mention the replacement scripts.
get_empty_ecs.pl  1.4  14 years  olson  Add license words.
get_empty_ecs  1.3  14 years  olson  Add license words.
get_dna.pl  1.6  11 years  gdpusch  Minor cosmetic change. -- /gdp
get_coupling_values.pl  1.3  9 years  overbeek  get rid of extraneous routine
get_class_examples.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_PSEED_assignment_updates.pl  1.5  8 years  olson  More fixups.
get_ON_probes.pl  1.3  8 years  olson  more fixes
get_NCBI_genome_attributes.pl  1.1  11 years  arodri7  get_NCBI_genome_attributes searches the NCBI internet sites for genome attribute...
get_FIGfams_SS_NMPDR_stats.pl  1.1  10 years  arodri7  *** empty log message ***
genomes_with_essentiality_data.pl  1.1  13 years  redwards  Adding tools to handle essentiality data for Sveta
genomes_of.pl  1.2  14 years  olson  Add license words.
genome_peg_dna.pl  1.3  12 years  golsen  Extensive modifications to allow more options, and handle large genomes by not r...
generate_subsys_tables_for_sprout.pl  1.8  14 years  olson  Add license words.
generate_sprout_links.pl  1.2  14 years  olson  Add license words.
generate_similarities.pl  1.3  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
generate_pinned_homologs.pl  1.2  14 years  olson  Add license words.
generate_pin_caches.pl  1.5  14 years  olson  Add license words.
generate_picked.pl  1.1  10 years  overbeek  stuff for gene calling
generate_partitions_worker.pl  1.4  9 years  disz  FigFam 6 digit problem
generate_partitionsP.pl  1.6  9 years  disz  FigFam 6 digit problem
generate_max_clusters.pl  1.2  14 years  olson  Add license words.
generate_kernel_css.pl  1.5  14 years  olson  Add license words.
generate_intergenic_blocks.pl  1.3  14 years  olson  Add license words.
generate_input_for_auto_assignments.pl  1.2  14 years  olson  Add license words.
generate_ilits.pl  1.3  9 years  olson  fix for FFs changes
generate_ilit_ev_codes.pl  1.4  11 years  overbeek  code relating to dlit/ilit maintenance
generate_genome_feature_tables_for_sprout.pl  1.16  14 years  olson  Add license words.
generate_gene_blocks.pl  1.3  14 years  olson  Add license words.
generate_dlit_ev_codes.pl  1.5  11 years  overbeek  switching to new ilidt/dlit stuff
generate_comparisons.pl  1.1  10 years  overbeek  stuff for gene calling
generate_Source_for_sprout.pl  1.2  14 years  olson  Add license words.
generate_Property_for_sprout.pl  1.6  14 years  olson  Add license words.
generate_GenomeGroups_for_sprout.pl  1.3  14 years  olson  Add license words.
generate_GO_attributes.pl  1.1  13 years  overbeek  add GO attribute genertation
genbank2gff3.pl  1.5  14 years  olson  Add license words.
genbank2fasta.pl  1.2  10 years  redwards  correcting ORIGIN regexp
gd_tree.pl  1.1  10 years  golsen  Add a command line program to make a png graphic from a newick tree file.
gather_genome_info.pl  1.2  10 years  olson  Add more data gathering
gather_attributes.pl  1.8  14 years  olson  Add license words.
fusion_of.pl  1.2  14 years  olson  Add license words.
functionally_coupled.pl  1.7  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
function_of.pl  1.5  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
format_peg_dbs.pl  1.3  14 years  olson  Add license words.
format_partition_dbs.pl  1.2  10 years  overbeek  try
form_clusters.pl  1.2  10 years  parrello  Final Server updates.
flip_sims.pl  1.7  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
flattened_to_fasta.pl  1.1  13 years  overbeek  add some minor utilities to flatten/unflatten fasta files
flatten_fasta.pl  1.1  13 years  overbeek  add some minor utilities to flatten/unflatten fasta files
flatten_attribute_files.pl  1.2  8 years  redwards  working on all subdirectories, not just a set of them
fix_invalid_fasta.pl  1.1  12 years  redwards  Initial release of programs to check and fix valid fasta format
fix_ext_funcs.pl  1.2  14 years  olson  Add license words.
fix_eol.pl  1.2  14 years  olson  Add license words.
fix_annotations.pl  1.2  14 years  olson  Add license words.
find_subsys.pl  1.3  11 years  overbeek  allow loose matching in rapid_propagation
find_special_proteins.pl  1.4  11 years  gdpusch  Suppress writing "called_by" and "special_pegs" when "-keep" is selected. -- /gd...
find_selenoproteins.pl  1.4  12 years  golsen  Add functions to reference selenoproteins, and add change the set slightly. Rep...
find_rnas.pl  1.2  9 years  olson  fix ANNOserver args
find_protein_homologs.pl  1.1  12 years  golsen  Debugging and adding support of all the NCBI genetic codes.
find_poss_fs.pl  1.1  12 years  overbeek  add code to fix frameshifts in a genome
find_poss_errs.pl  1.3  9 years  disz  FigFam 6 digit problem
find_neighbors_using_figfams.pl  1.11  10 years  olson  Switch to FFs and FF instead of FigFams and FigFam
find_neighbors_by_sim.pl  1.4  11 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
find_neighbors.pl  1.39  9 years  disz  FigFam 6 digit problem
find_model_information_v2.pl  1.2  11 years  dejongh  switch to scenario_directory
find_model_information.pl  1.7  11 years  dejongh  switch to scenario_directory
find_model_cofactors.pl  1.7  11 years  dejongh  switch to scenario_directory
find_missing_lib_inputs_v2.pl  1.2  11 years  dejongh  switch to scenario_directory
find_missing_lib_inputs.pl  1.6  11 years  dejongh  switch to scenario_directory
find_missing_genes.pl  1.10  9 years  olson  more RAST fixes (some of these may need to be backported to use the SAP version ...
find_miscalled_genes.pl  1.4  9 years  gdpusch  Added check to make sure nonref gene is not already in a subsystem.
find_maximal_clusters.pl  1.2  14 years  olson  Add license words.
find_genes_in_families.pl  1.22  10 years  olson  Switch to FFs and FF instead of FigFams and FigFam
find_genes_based_on_neighbors_par.pl  1.1  9 years  olson  parallel version of find_genes_based_on_neighbors
find_genes_based_on_neighbors.pl  1.24  10 years  olson  Switch to FFs and FF instead of FigFams and FigFam
find_genes_based_on_kmers.pl  1.9  8 years  olson  More fixups.
find_gaps.pl  1.9  10 years  gdpusch  Fixed (hopefully) incorrectly handled out-of-bounds cases.
find_essential_reactions.pl  1.3  11 years  dejongh  switch to scenario_directory
find_bad_conflicts.pl  1.1  13 years  overbeek  fixes to wseekly statistics
find_approx_neigh.pl  1.6  8 years  gdpusch  Modified to look for "proposed_functions" and "proposed_non_ff_functions" as wel...
find_SEED_SSU_rRNA_genes.pl  1.4  10 years  golsen  Add type field to output report (always rna).
filter_trunc_and_fs.pl  1.2  9 years  olson  Add SeedUtils::map_to_families for iterating over families.2c files. Make filte...
filter_tbl_overlaps.pl  1.10  13 years  overbeek  set up find_neighbors to handle existing genomes
filter_pegs_in_subsystems.pl  1.4  14 years  olson  Add license words.
filter_overlaps.pl  1.5  13 years  overbeek  Added some more diagnosting lines. -- /gdp
filter_on_known.pl  1.1  9 years  overbeek  filter pegs with no raw data
filter_new_overlaps.pl  1.2  14 years  olson  Add license words.
filter_figfams.pl  1.2  12 years  overbeek  add computation of alignments to building FIGFAMS
filter_and_merge_gene_sets.pl  1.2  8 years  overbeek  merge is better
fill_subsys.pl  1.5  14 years  olson  Add license words.
fill_in_roles.pl  1.4  14 years  olson  Add license words.
fill_in_cell.pl  1.2  14 years  olson  Add license words.
figfam_subsystems.pl  1.2  10 years  arodri7  commit changes
figfam_size_distribution.pl  1.1  11 years  arodri7  update changes
figfam_quality_control.pl  1.8  10 years  arodri7  commit changes
figfam.pl  1.23  9 years  disz  FigFam 6 digit problem
fig_xmlrpc_server.pl  1.5  14 years  olson  Add license words.
fig_specific_sequences.pl  1.3  13 years  redwards  using is_environmental instead of seven 9s
fig_rpc.pl  1.4  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...
fig.pl  1.155  8 years  redwards  adding a method to list all phages
fid2dna.pl  1.2  14 years  olson  Add license words.
ff.pl  1.7  9 years  disz  FigFam 6 digit problem
fetch_models_for_genomes.pl  1.1  8 years  fangfang  initial import
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...
feature_length_histogram.pl  1.3  12 years  gdpusch  Fixed duplicated ID bug, plus minor cosmetic changes. -- /gdp
fc_figfams.pl  1.3  9 years  disz  FigFam 6 digit problem
fastasize.c  1.3  14 years  olson  Doh, put proper comments in for C code.
fasta_to_phylip.pl  1.2  14 years  olson  Add license words.
fasta_size.pl  1.1  10 years  overbeek  add fasta_size
fasta_for_hypo.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.
fast_blastp.pl  1.1  11 years  overbeek  fast_blastp is a tool to support rapid similarity estimates using FIGfam partiti...
fabric_vec.pl  1.1  10 years  overbeek  add ability to make fabric vecs
extract_subset_from_sprout_data.pl  1.2  14 years  olson  Add license words.
extract_sp_links.pl  1.3  13 years  olson  fix -h error
extract_metagene_contigs.pl  1.12  9 years  gdpusch  Updated search for executables to revised software environment.
extract_genomes.pl  1.38  13 years  overbeek  changes to support dynamic sims and updates
extract_genes.pl  1.5  14 years  olson  Add license words.
extract_fasta_idmap.pl  1.1  13 years  overbeek  RAE: Adding FigKernelScripts/extract_fasta_idmap.pl
extract_data_to_keep.pl  1.5  14 years  olson  Add license words.
extract_data_for_syncing_after_update.pl  1.6  14 years  olson  Add license words.
extract_DNA_sequence_from_object_for_start_predictions.pl  1.2  14 years  olson  Add license words.
extract_DNA_for_whole_ORFs.pl  1.4  10 years  gdpusch  Fixed possible DNA case sensitivity.
external_calls.pl  1.2  14 years  olson  Add license words.
extend_subsystem.pl  1.2  14 years  olson  Add license words.
extend_subsys.pl  1.7  13 years  redwards  using is_environmental instead of seven 9s
export_subsystem_as_gff.pl  1.2  14 years  olson  Add license words.
export_similarity_request.pl  1.3  13 years  overbeek  minor fixes to assignment for close strains
export_phage_data.pl  1.1  8 years  redwards  two phage specific scripts
export_genome_as_gff.pl  1.6  14 years  olson  Add license words.
export_dlits.pl  1.2  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
export_ACH_resolution_DB.pl  1.2  11 years  overbeek  fixes relating to comments
explore_subsys_pmid.pl  1.5  12 years  hwang  PEG information is no longer stored in the file. Parsing of the file in this scr...
expand_transferred_chunks.pl  1.4  14 years  olson  Add license words.
expand_sims.pl  1.2  11 years  olson  *** empty log message ***
expand_multifunctional_roles.pl  1.3  14 years  olson  Add license words.
expand_blast_table.pl  1.2  14 years  olson  Add license words.
exec-cgi.pl  1.1  9 years  olson  cgi executor for mac rast
exclude_genomes.pl  1.3  11 years  parrello  Fixed a POD error.
evaluate_quality_of_trees.pl  1.4  12 years  overbeek  debugged version of bring_tree_up_to_ali
ev_code_cron.pl  1.16  11 years  parrello  Updated comments to mention the replacement scripts.
estimated_fabric.pl  1.1  10 years  overbeek  code for processing fabrics and population estimates
ensure_genome_registration.pl  1.1  12 years  olson  generate feature registration stuff
embl2gff_addmd5.py  1.2  14 years  olson  Add license words.
embl2gff.pl  1.20  14 years  olson  Add license words.
dump_ss_classification.pl  1.1  11 years  redwards  adding ss classification methods
dump_machine_state.pl  1.3  14 years  olson  Add license words.
dump_attributes.pl  1.2  14 years  olson  Add license words.
dp.pl  1.4  10 years  redwards  editing header info
dna_seq.pl  1.2  14 years  olson  Add license words.
distribute_attributes.pl  1.11  14 years  olson  Add license words.
display_tree.pl  1.4  14 years  olson  Add license words.
direct_functional_coupling.pl  1.4  12 years  overbeek  tighten length constraints for figfam matching
difference_between_two_databases.pl  1.1  10 years  redwards  code for generating the delta between two databases
diff_tbls.pl  1.1  13 years  overbeek  Computes difference betwween two tbl files. -- /gdp
delete_genomes_from_sims.pl  1.2  14 years  olson  Add license words.
delete_all_attribute_files.pl  1.2  13 years  overbeek  RAE: New delete attribute files to remove all files. maybe this will work
db_xrefs_of.pl  1.4  14 years  olson  Add license words.
das_test.pl  1.2  14 years  olson  Add license words.
curator_of.pl  1.1  13 years  overbeek  minor fixes to assignment for close strains
create_sims_btree.pl  1.1  13 years  olson  BTREE-index versions of these. Experimental still.
create_ff_covering_skeleton.pl  1.2  10 years  arodri7  fixed script that creates a directory structure for a FIGfam for its sequence co...
createTIGRfamSrc.pl  1.1  11 years  bartels  *** empty log message ***
crc64.py  1.1  11 years  mkubal  uses for mapping of interpro downlaod to pegs
count_bases.pl  1.2  14 years  olson  Add license words.
correct_gff_missing_contigs.pl  1.5  12 years  redwards  correcting a weird error
correct_frameshifts.pl  1.25  8 years  gdpusch  Replaced dies with warn and exit if '-nofatal', so that script fails gracefully ...
corr_build_connections.pl  1.1  8 years  parrello  New stuff for Salmonella sets.
convert-blast-to-m8.pl  1.1  10 years  olson  Convert full blast output to -m8 output using Gary's blast parsing code.
connections_between.pl  1.8  10 years  overbeek  fixes to making close strain data
connect_PDB_to_FIGfams_worker.pl  1.1  11 years  arodri7  update changes
connect_PDB_to_FIGfams.pl  1.1  11 years  arodri7  update changes
conditionally_assign.pl  1.5  11 years  overbeek  get rid of warning and update conditionally_assign
condense_blast.pl  1.2  14 years  olson  Add license words.
compute_translation_MD5.c  1.3  8 years  redwards  ignoring stops
compute_simple_scores.pl  1.4  14 years  olson  Add license words.
compute_sim_chunk.pl  1.3  13 years  olson  add working-on-chunk support
compute_potential_fusions.pl  1.12  13 years  overbeek  fix to fusions
compute_pins_and_clusters.pl  1.2  14 years  olson  Add license words.
compute_pins.pl  1.4  11 years  olson  undo bogus commit
compute_pchs_from_sims.pl  1.2  12 years  olson  Rollup of changes for the new RAST install.
compute_pc.pl  1.1  9 years  overbeek  code from Hope
compute_new_ids.pl  1.2  14 years  olson  Add license words.
compute_mw_and_pi_with_BioPerl.pl  1.1  12 years  mkubal  computes mw and pi for all pegs in complete genomes
compute_mw_and_pi.pl  1.2  12 years  mkubal  one genome at a time
compute_genome_similarity.pl  1.1  12 years  olson  Missing scripts.
compute_genome_counts.pl  1.25  10 years  olson  Fix bug where compute_genome_counts fails to run on a genome directory with mult...
compute_figfam_assignments.pl  1.2  9 years  olson  Clean up debugging, write concatenated output file.
compute_fasta_lengths.pl  1.1  9 years  olson  Precompute fasta lengths for the non-FF nr.
compute_extra_dlit_data.pl  1.4  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
compute_ev_code_attributes.pl  1.2  11 years  overbeek  do not include cluster-based subsystems in forming evidence codes
compute_dbdir_checksum.pl  1.3  13 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
compute_crc64_for_all_pegs.pl  1.1  12 years  mkubal  v1
compute_contig_md5.pl  1.4  12 years  olson  rollup of metagenome server changes
compute_changed_ids_for_nrs.pl  1.5  10 years  olson  misc fixes
compute_atomic_regulons_for_dir.pl  1.2  8 years  overbeek  loosen threshhold of mismatches
compute_atomic_regulons.pl  1.2  9 years  overbeek  compute atomic regulons only for new data
compute_PSEED_reconstructions.pl  1.2  8 years  olson  More fixups.
compute_PCA_with_metagenomes_as_variables.pl  1.1  10 years  mkubal  called by PCA_mgav
compute_PCA_for_metagenomes.pl  1.1  10 years  mkubal  called by PCA_ssav
compute_CELLO_and_TMPRED.pl  1.2  12 years  mkubal  test for dir exist
complete_genomes.pl  1.7  14 years  olson  Add license words.
compare_two_sets_of_calls.pl  1.3  10 years  overbeek  stuff for gene calling
compare_tree_and_alignment.pl  1.2  14 years  olson  Add license words.
compare_tbls.pl  1.5  13 years  overbeek  Minor change to output. -- /gdp
compare_scenarios.pl  1.5  11 years  dejongh  Changes to move the 'All' scenarios directory to FIG_Config::global/Models/All
compare_figfam_release_results.pl  1.5  10 years  arodri7  commit changes
compareMR.pl  1.1  12 years  overbeek  basic stuff for comparing metabolic reconstructions
collect_related_sequences.pl  1.3  12 years  golsen  Encapsulate all of the SEED-dependent functions in the perl module. It should st...
clustered_hypotheticals.pl  1.2  9 years  overbeek  major rewrite
cluster_objects.pl  1.5  8 years  overbeek  require connections to begin each line
cluster_exp.pl  1.1  9 years  overbeek  cluster experiments into states
cluster_by_sim.pl  1.2  14 years  olson  Add license words.
cluster_by_bbhs.pl  1.2  14 years  olson  Add license words.
clustal_to_fasta.pl  1.2  14 years  olson  Add license words.
clustal2fasta.pl  1.2  14 years  olson  Add license words.
close_connections.pl  1.2  12 years  overbeek  add strip comments argument on function_of
cleanup_figfams_updates.pl  1.1  10 years  arodri7  commit changes
clean_subsystems.pl  1.2  14 years  olson  Add license words.
clean_sims.pl  1.2  14 years  olson  Add license words.
check_tbl.pl  1.2  14 years  olson  Add license words.
check_subsystems.pl  1.7  12 years  overbeek  strip comments on functions for subsystem checking
check_subs_and_split_warnings.pl  1.3  11 years  overbeek  minor fix to handle deleted subsystems
check_starts_for_pegs.pl  1.5  14 years  olson  Add license words.
check_starts_for_peg_sets.pl  1.5  14 years  olson  Add license words.
check_sims_syntax.pl  1.3  14 years  olson  Add license words.
check_sims_basic.pl  1.8  13 years  redwards  using is_environmental instead of seven 9s
check_peg_placement.pl  1.1  12 years  overbeek  redone FIGfam stuff
check_peg_assignments.pl  1.3  14 years  olson  Add license words.
check_nr_and_peg_synonyms.pl  1.2  14 years  olson  Add license words.
check_model_v2.pl  1.2  11 years  dejongh  switch to scenario_directory
check_model.pl  1.7  11 years  dejongh  switch to scenario_directory
check_lost_sims.pl  1.2  14 years  olson  Add license words.
check_hope_info.pl  1.8  9 years  dejongh  updates to check for invalid maps and reaction/ec mismatches
check_for_unique_sims.pl  1.2  14 years  olson  Add license words.
check_for_scenario_reachability.pl  1.3  11 years  dejongh  switch to scenario_directory
check_for_possible_mobile_elements.pl  1.1  12 years  overbeek  add code to search for mobile elements
check_for_new_genomes.pl  1.3  10 years  overbeek  print stats as you go
check_figfams.pl  1.6  11 years  olson  Introduct &FIG::get_figfams_data()
check_fasta_for_dups.pl  1.1  12 years  olson  Missing scripts.
check_fast_sims.pl  1.2  14 years  olson  Add license words.
check_consistency_of_sample.pl  1.7  10 years  redwards  correcting looping through parts of the genomes
check_changes_in_organisms.pl  1.2  14 years  olson  Add license words.
check_and_extend_all_subsystems.pl  1.7  13 years  overbeek  fix call to rapid_subsystem_extension in check_and_extend_all_subsystems
check_all_subsystems.pl  1.11  11 years  olson  Transform the single big select into a prepared statement on per-role select.s
check_all_lost_sims.pl  1.2  14 years  olson  Add license words.
check_alignment.pl  1.2  14 years  olson  Add license words.
changed_starts.pl  1.7  14 years  olson  Add license words.
cat_spreadsheet.pl  1.2  14 years  olson  Add license words.
call_genome_using_glimmer.pl  1.3  10 years  gdpusch  Rewrite to remove overlap removal.
call_genes.pl  1.4  9 years  olson  fix ANNOserver args
call_coregulated_clusters_on_chromosome.pl  1.7  8 years  olson  Update to expression pipeline code
cache_comparison_data.pl  1.11  10 years  paczian  fixed load order of function files in RAST vs SEED organisms
build_syn.pl  1.2  14 years  olson  Add license words.
build_sets_from_clusters.pl  1.2  8 years  parrello  Minor fixes for debugging.
build_sas_distro_from_cvs.pl  1.2  9 years  olson  mods for building myRAST
build_sas_distro.pl  1.7  9 years  olson  mods for building myRAST
build_protein_families.pl  1.5  14 years  olson  Add license words.
build_prok_nonff_fasta.pl  1.4  9 years  disz  FigFam 6 digit problem
build_partition_index.pl  1.1  11 years  overbeek  return empty list of failure to open FIFfam
build_nr_sources.pl  1.14  12 years  olson  Rollup of various rast-related changes.
build_nr.pl  1.22  11 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
build_nohit_fasta.pl  1.2  14 years  olson  Add license words.
build_new_figfam_release.pl  1.5  9 years  disz  FigFam 6 digit problem
build_initial_objects_for_start_predictions.pl  1.12  11 years  gdpusch  Modified to also work on new genomes using "FIGV.". -- /gdp
build_figfam_pssm_db.pl  1.2  12 years  gdpusch  Major modifications to &load_family_ids()
build_exemplar_fasta.pl  1.3  14 years  olson  Add license words.
build_excel_gene_table.pl  1.3  14 years  olson  Add license words.
build_dtr_distro.pl  1.1  8 years  olson  new script
build_anno_clearinghouse.pl  1.6  11 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
build_all_prok_seqs.pl  1.1  9 years  overbeek  get all protein sequences for complete prokaryotic genomes
build_alignments_from_spreadsheet.pl  1.7  13 years  redwards  using is_environmental
build_alignments_for_subsystems.pl  1.4  14 years  olson  Add license words.
build_access_sets.pl  1.2  14 years  olson  Add license words.
bring_tree_up_to_ali.pl  1.5  12 years  overbeek  debugged version of bring_tree_up_to_ali
bring_system_up_to_date.pl  1.2  14 years  olson  Add license words.
break_scaffolds.pl  1.2  14 years  olson  Add license words.
boot_cluster_seed.pl  1.5  13 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
blastp_pseq.pl  1.6  10 years  redwards  adding a default cutoff
blastn_seqs.pl  1.2  14 years  olson  Add license words.
blastn_chunks.pl  1.3  12 years  overbeek  initial, undebugged version of edit_feature.cgi
blast_request.pl  1.2  14 years  olson  Add license words.
blast_pdb_against_nr_on_tla.pl  1.1  12 years  mkubal  blast pdb against nr
blastP.pl  1.1  10 years  olson  Switch to using assign_functions_to_prot_set in assign_using_kmers.pl. Add blast...
blast2gff.pl  1.23  9 years  redwards  adding an option for gziped files
bielefeld_tarfile_to_seed.pl  1.7  13 years  overbeek  Tweaked usage msg. -- /gdp
best_tree_using_proml_on_cluster.pl  1.1  12 years  overbeek  add best_tree_using_proml_on_cluster
best_hits.pl  1.2  14 years  olson  Add license words.
bbhs.pl  1.7  14 years  olson  Add license words.
bayes_expected_start_scores.pl  1.3  12 years  overbeek  Added comments to expalin logic. -- gdp
backup_subsystems.pl  1.3  11 years  parrello  Fixed a POD error.
backup_critical_data.pl  1.5  10 years  olson  fix bug that kept subsystems from being backedup
backfill_gaps.pl  1.20  9 years  gdpusch  Added check to make sure comparison genome exists, in case RAST and OTU servers ...
auto_assign.pl  1.19  11 years  olson  Add -orgdir option to use FIGV and its indexed sims.
at.pl  1.3  8 years  fangfang  update
assign_with_no_sims.pl  1.2  14 years  olson  Add license words.
assign_using_kmers.pl  1.8  9 years  olson  Add support for explicitly specifying FRI.db, setI.db, table.binary
assign_using_ff_parallel.pl  1.2  10 years  arodri7  made updates to functions used for updating FIGfams
assign_using_ff_original.pl  1.1  10 years  arodri7  original format of assign_using_ff
assign_using_ff.pl  1.9  10 years  arodri7  commit changes
assign_towards_subsystems.pl  1.2  14 years  olson  Add license words.
assign_to_unchanged.pl  1.3  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
assign_to_sets.pl  1.5  14 years  olson  Add license words.
assign_to_hypo.pl  1.3  14 years  olson  Add license words.
assign_to_dna_using_kmers.pl  1.5  10 years  olson  more anno server fixes, add some missing files
assign_to_close_strains.pl  1.10  13 years  overbeek  fixes to Assignments.pm
assign_synonym_ids_to_sims.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.pl  1.2  14 years  olson  Add license words.
assign_figfam.pl  1.1  10 years  arodri7  add original assign_using_ff
assign.pl  1.2  14 years  olson  Add license words.
assess_gene_call_quality.pl  1.14  9 years  olson  don't write the overlap report to metadata log; it is very large.
assess_completeness.pl  1.9  11 years  gdpusch  Fixed leading-whitspace bug.
are_close.pl  1.1  13 years  overbeek  fixes to extract_genomes
apply_peg_changes_to_subsystem.pl  1.3  14 years  olson  Add license words.
apply_map.pl  1.2  14 years  olson  Add license words.
analyze_scenario_connections.pl  1.4  11 years  dejongh  Changes to move the 'All' scenarios directory to FIG_Config::global/Models/All
analyze_kmer_assignments.pl  1.1  10 years  olson  new script to compare output of assign_using_kmers to current SEED assignments
alter_tbl.pl  1.4  14 years  olson  Add license words.
all_subsystems.pl  1.2  14 years  olson  Add license words.
all_bbhs.pl  1.16  12 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
alignment_to_html.pl  1.2  9 years  golsen  Minor updates.
align_with_clustal_2.pl  1.4  12 years  golsen  Trivial format change.
align_with_clustal.pl  1.8  14 years  olson  Add license words.
align_seqs.pl  1.1  12 years  overbeek  add utilities for computing alignments
align_fasta.pl  1.3  9 years  golsen  Add support for alignment with muscle.
aliases_of.pl  1.6  14 years  olson  Add license words.
alias2fig.pl  1.2  14 years  olson  Add license words.
ali_tree.pl  1.4  12 years  overbeek  add strip comments argument on function_of
ali_to_seq.pl  1.2  14 years  olson  Add license words.
adjacent.pl  1.3  12 years  redwards  changing chop to chomp
add_to_subsystems.pl  1.1  13 years  overbeek  add add_to_subsystems
add_to_alignment.pl  1.8  8 years  golsen  Fix the libraries used for I/O.
add_structured_english.pl  1.4  11 years  disz  Added escape arg to structured engkish
add_start_data_for_start_predictions.pl  1.4  12 years  gdpusch  Added FIGV support. -- /gdp
add_sim_data_for_start_predictions.pl  1.8  12 years  gdpusch  Added FIGV support. -- /gdp
add_rbs_data_for_start_predictions.pl  1.3  12 years  gdpusch  Added FIGV support. -- /gdp
add_prots_to_tree.pl  1.1  12 years  golsen  New script for adding proteins to an existing tree.
add_figbar_and_genome_attributes.pl  1.1  12 years  mkubal  v1
add_close_genes.pl  1.2  14 years  olson  Add license words.
add_attributes_from_file.pl  1.1  12 years  redwards  just a simple attribute loader
add_assignments.pl  1.3  14 years  olson  Add license words.
add_assertions_of_function.pl  1.38  9 years  olson  add assignment logging, index on org.
aclh_reload_contrib.pl  1.2  10 years  wilke  added db handle in ach call
aclh.pl  1.11  11 years  paarmann  added new parameter to dump contribs
accumulate_pegs_to_scenario_paths.pl  1.1  8 years  dejongh  determine which pegs in an organism are involved in which scenario paths
WikiMaker.pl  1.6  11 years  parrello  Added more trace messages.
WebAppBackend.pl  1.2  10 years  jared  make user and org commands case insensitive
TransactFeatures.pl  1.20  11 years  parrello  Removed obsolete use clause.
Tracer.pl  1.1  11 years  parrello  New script used to route STDERR messages to the trace log.
TestLocations.pl  1.8  11 years  parrello  Converted to use new name for Contrain method.
SplitGeneSets.R  1.2  8 years  olson  Update to expression pipeline code
SpanishInquisition.pl  1.1  11 years  parrello  Added for testing the Confess method.
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...
ShewanellaRMA.R  1.1  9 years  overbeek  code from Hope
RunRMA_SIF_format.R  1.1  8 years  olson  SIF-processing run-rma.
RunRMA.R  1.5  8 years  dejongh  preallocate no_match_pm_mm; delete no_match row at end
README  1.1.1.1  16 years  efrank   import
Pipeline.R  1.4  8 years  olson  Update to expression pipeline code
PickGeneBoundariesTest.pl  1.1  11 years  parrello  Test script for backfill.
Packager.pl  1.7  12 years  parrello  Changed POD format for better compatability with Wiki.
OneShotAttributeAdder.pl  1.2  11 years  parrello  Removed obsolete use clauses.
NMPDRAnalysis.pl  1.5  11 years  parrello  Removed obsolete use clauses.
Makefile.cprogs  1.2  12 years  olson  Support compilation of nap.c
Makefile  1.24  8 years  olson  fix R build target. why it works for me and not elsewhere I don't know
ListLits.pl  1.1  11 years  parrello  New script to count literature references for NMPDR.
LigandCleanup.pl  1.2  11 years  parrello  Removed obsolete use clases.
GeneSet_P_Values.R  1.3  8 years  dejongh  fixes
FIGMODELscheduler.pl  1.3  9 years  chenry  Switched over the PPO as the system for holding the job queue tables.
FFB2_xy.pl  1.1  9 years  olson  Update to FF processing
FFB2_xx.pl  1.1  9 years  olson  Bunch of figfam generation optimizations.
FFB2_validate_families.pl  1.1  9 years  olson  Update to FF processing
FFB2_usable_motifs2.pl  1.3  8 years  olson  Update to figfam build code
FFB2_usable_motifs.pl  1.4  9 years  olson  Update to FF processing
FFB2_update_FIGfams.pl  1.16  9 years  olson  fix memcache stuff
FFB2_split_fams_by_size.pl  1.2  9 years  olson  Big round of figfam update changes
FFB2_run_tests.pl  1.3  8 years  olson  Update to figfam build code
FFB2_merge_oligos.pl  1.4  9 years  olson  Update to FF processing
FFB2_merge_families_based_on_genus_groups.pl  1.3  9 years  olson  Big round of figfam update changes
FFB2_make_subsys_based_families.pl  1.3  9 years  olson  Big round of figfam update changes
FFB2_make_family_vector.pl  1.1  8 years  olson  compute family.vector.def for a figfam direcotry.
FFB2_make_FF_index.pl  1.2  9 years  olson  Rollup of figfam update fixes
FFB2_load_oligo_index.pl  1.1  10 years  overbeek  new scripts for updating FIGfams and Kmer tables
FFB2_load_memcache.pl  1.7  8 years  olson  Update to figfam build code
FFB2_install_kmers.pl  1.2  9 years  olson  Update to FF processing
FFB2_get_prots.pl  1.3  9 years  olson  Bunch of figfam generation optimizations.
FFB2_get_prot_gs_oligos.pl  1.1  10 years  overbeek  new scripts for updating FIGfams and Kmer tables
FFB2_get_oligos2.pl  1.3  8 years  olson  Update to figfam build code
FFB2_get_oligos.pl  1.10  9 years  disz  FigFam 6 digit problem
FFB2_genome_group_pipeline.pl  1.1  9 years  olson  New FIGfam merge code.
FFB2_families_in_subsystems.pl  1.1  9 years  olson  Update to FF processing
FFB2_create_binary_relationships.pl  1.1  9 years  olson  New FIGfam merge code.
FFB2_create_binary_kmers.pl  1.6  8 years  olson  Update to figfam build code
FFB2_compute_relationships_for_genera.pl  1.1  9 years  olson  New FIGfam merge code.
FFB2_compare_to_anno3.pl  1.2  9 years  olson  fixes for release names
FFB2_compare_tests.pl  1.4  8 years  olson  Update to figfam build code
FFB2_build_updated_FF.pl  1.23  8 years  olson  Update to figfam build code
FFB2_build_ff_indexes.pl  1.1  9 years  olson  Rollup of figfam update fixes
EmergencyMapFlipper.pl  1.2  9 years  parrello  *** empty log message ***
EcoliRMA.R  1.2  9 years  overbeek  from Matt
Consistency_Families.pm  1.1  11 years  bartels  *** empty log message ***
CheckCELfiles.R  1.1  9 years  olson  R script to find chip name from CEL files
COPYING.TXT  1.1  14 years  olson  add license file

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