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File Rev. Age Author Last log entry
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BuildCodonUsageExchAndLoadFiles.pl  1.1  6 years  golsen  Build files to support moving codon usage data into KBase.
COPYING.TXT  1.1  12 years  olson  add license file
CSA_build_alignments.pl  1.17  6 years  overbeek  allow option to preserve sequence order
CSA_close_strains.pl  1.8  7 years  overbeek  sort space in this directory
CSA_collapse_repeats.pl  1.3  7 years  overbeek  make sorts in local dir, not /tmp
CSA_create_SNP_data.pl  1.7  5 years  overbeek  compute correspondences for a pan genome
CSA_filter_unique.pl  1.2  7 years  overbeek  make part of myRAST distribution
CSA_first_pass.pl  1.4  7 years  overbeek  remove dependency on BasicLocation
CSA_gather_mapped_objects.pl  1.2  7 years  overbeek  make part of myRAST distribution
CSA_get_close_strain_annotations.pl  1.5  7 years  overbeek  spelling errors
CSA_get_repeat_dna.pl  1.2  7 years  overbeek  make part of myRAST distribution
CSA_layout.pl  1.2  7 years  overbeek  make part of myRAST distribution
CSA_make_conn.pl  1.2  7 years  overbeek  make part of myRAST distribution
CSA_make_contig_index.pl  1.2  7 years  overbeek  make part of myRAST distribution
CSA_make_unique_kmers.pl  1.4  7 years  overbeek  make sorts in local dir, not /tmp
CSA_merge_estimates.pl  1.8  7 years  overbeek  add translations to features
CSA_predict_features_based_on_refs.pl  1.1  7 years  overbeek  minor fixes
CSA_ref_vs_ref.pl  1.6  6 years  overbeek  extra comments
CSA_second_pass.pl  1.4  7 years  overbeek  fix coordinates within alignments
CS_build_fasta_for_phylogeny.pl  1.6  4 years  overbeek  take gids from genome.names
CS_compute_coupling.pl  1.5  4 years  overbeek  take gids from genome.names
CheckCELfiles.R  1.1  8 years  olson  R script to find chip name from CEL files
Consistency_Families.pm  1.1  10 years  bartels  *** empty log message ***
EcoliRMA.R  1.2  8 years  overbeek  from Matt
EmergencyMapFlipper.pl  1.2  8 years  parrello  *** empty log message ***
EmergencySubsystemFix.pl  1.2  7 years  parrello  Bug fix in index_subsystems call.
FFB2_build_ff_indexes.pl  1.1  8 years  olson  Rollup of figfam update fixes
FFB2_build_updated_FF.pl  1.24  5 years  olson  Update to figfam processing
FFB2_compare_tests.pl  1.4  7 years  olson  Update to figfam build code
FFB2_compare_to_anno3.pl  1.2  8 years  olson  fixes for release names
FFB2_compute_relationships_for_genera.pl  1.1  8 years  olson  New FIGfam merge code.
FFB2_create_binary_kmers.pl  1.6  7 years  olson  Update to figfam build code
FFB2_create_binary_relationships.pl  1.1  8 years  olson  New FIGfam merge code.
FFB2_families_in_subsystems.pl  1.1  8 years  olson  Update to FF processing
FFB2_genome_group_pipeline.pl  1.1  8 years  olson  New FIGfam merge code.
FFB2_get_oligos.pl  1.10  8 years  disz  FigFam 6 digit problem
FFB2_get_oligos2.pl  1.4  5 years  olson  Update to figfam processing
FFB2_get_prot_gs_oligos.pl  1.1  8 years  overbeek  new scripts for updating FIGfams and Kmer tables
FFB2_get_prots.pl  1.3  8 years  olson  Bunch of figfam generation optimizations.
FFB2_install_kmers.pl  1.2  8 years  olson  Update to FF processing
FFB2_load_memcache.pl  1.7  7 years  olson  Update to figfam build code
FFB2_load_oligo_index.pl  1.1  8 years  overbeek  new scripts for updating FIGfams and Kmer tables
FFB2_make_FF_index.pl  1.3  5 years  olson  Update to figfam processing
FFB2_make_family_vector.pl  1.1  7 years  olson  compute family.vector.def for a figfam direcotry.
FFB2_make_subsys_based_families.pl  1.3  7 years  olson  Big round of figfam update changes
FFB2_merge_and_build_kmers.pl  1.1  5 years  olson  Update to figfam processing
FFB2_merge_families_based_on_genus_groups.pl  1.3  7 years  olson  Big round of figfam update changes
FFB2_merge_oligos.pl  1.4  8 years  olson  Update to FF processing
FFB2_pull_extreme_FF_members.pl  1.2  5 years  olson  Update to figfam processing
FFB2_run_tests.pl  1.3  7 years  olson  Update to figfam build code
FFB2_split_fams_by_size.pl  1.3  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
FFB2_update_FIGfams.pl  1.17  5 years  olson  Update to figfam processing
FFB2_usable_motifs.pl  1.4  8 years  olson  Update to FF processing
FFB2_usable_motifs2.pl  1.3  7 years  olson  Update to figfam build code
FFB2_validate_families.pl  1.1  8 years  olson  Update to FF processing
FFB2_xx.pl  1.1  8 years  olson  Bunch of figfam generation optimizations.
FFB2_xy.pl  1.1  8 years  olson  Update to FF processing
FFB3_assemble_translations.pl  1.2  5 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_build_ff_indexes.pl  1.1  6 years  olson  New figfam building code.
FFB3_build_ff_oligos.pl  1.1  6 years  olson  New figfam building code.
FFB3_build_otu_oligos.pl  1.1  6 years  olson  New figfam building code.
FFB3_build_updated_FF.pl  1.5  5 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_cleanup_families.pl  1.1  5 years  olson  Favor non-blank functions in FFB3_update_FIGfams::function_of_family Add new scr...
FFB3_compare_tests.pl  1.1  6 years  olson  New figfam building code.
FFB3_construct_assigned_functions.pl  1.2  5 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_create_binary_kmers.pl  1.1  6 years  olson  New figfam building code.
FFB3_families_to_fasta.pl  1.1  6 years  olson  New figfam building code.
FFB3_get_gs_oligos.pl  1.1  6 years  olson  New figfam building code.
FFB3_get_oligos.pl  1.1  6 years  olson  New figfam building code.
FFB3_get_recent_annotations.pl  1.2  5 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_load_oligo_index.pl  1.1  6 years  olson  New figfam building code.
FFB3_make_subsys_based_families.pl  1.2  5 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_make_subsys_based_families_2.pl  1.1  6 years  olson  New figfam building code.
FFB3_merge_and_build_kmers.pl  1.1  6 years  olson  New figfam building code.
FFB3_merge_families_by_kmers.pl  1.1  6 years  olson  roundup of figfam build changes
FFB3_package_figfams.pl  1.1  6 years  olson  New figfam building code.
FFB3_run_parallel_usable_motifs.pl  1.1  6 years  olson  New figfam building code.
FFB3_run_tests.pl  1.1  6 years  olson  New figfam building code.
FFB3_set_figfam_functions.pl  1.2  5 years  olson  Update to figfam processing
FFB3_update_FIGfams.pl  1.2  5 years  olson  Favor non-blank functions in FFB3_update_FIGfams::function_of_family Add new scr...
FFB3_usable_motifs.pl  1.1  6 years  olson  New figfam building code.
FIGMODELscheduler.pl  1.3  8 years  chenry  Switched over the PPO as the system for holding the job queue tables.
GTO_to_PGF_genome_stats.pl  1.1  20 months  jdavis  Adding GTO_to_PGF_genome_stats.pl
GeneSet_P_Values.R  1.3  7 years  dejongh  fixes
GenomeTypeObject.t  1.1  3 years  olson  Initial genome type object tester
LigandCleanup.pl  1.2  10 years  parrello  Removed obsolete use clases.
ListLits.pl  1.1  10 years  parrello  New script to count literature references for NMPDR.
Makefile  1.31  4 years  olson  Fix the broken stuff (bob commented out some lines erroneously)
Makefile.cprogs  1.2  10 years  olson  Support compilation of nap.c
NMPDRAnalysis.pl  1.5  10 years  parrello  Removed obsolete use clauses.
OneShotAttributeAdder.pl  1.2  10 years  parrello  Removed obsolete use clauses.
Packager.pl  1.7  10 years  parrello  Changed POD format for better compatability with Wiki.
PickGeneBoundariesTest.pl  1.1  10 years  parrello  Test script for backfill.
Pipeline.R  1.4  7 years  olson  Update to expression pipeline code
README  1.1.1.1  14 years  efrank   import
RunRMA.R  1.5  7 years  dejongh  preallocate no_match_pm_mm; delete no_match row at end
RunRMA_SIF_format.R  1.1  7 years  olson  SIF-processing run-rma.
SStest.pl  1.1  4 years  parrello  CDMI and Sprout load fixes. Locations fixes.
ShewanellaRMA.R  1.1  8 years  overbeek  code from Hope
Simple.pl  1.4  12 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
SpanishInquisition.pl  1.1  10 years  parrello  Added for testing the Confess method.
SplitGeneSets.R  1.2  7 years  olson  Update to expression pipeline code
SwissProtJSON_to_loadfile.pl  1.1  2 years  golsen  Create wrapper program SwissProtXML_to_JSON for the XML to JSON; includes abilit...
SwissProtXML_to_JSON.pl  1.1  2 years  golsen  Create wrapper program SwissProtXML_to_JSON for the XML to JSON; includes abilit...
TestLocations.pl  1.8  10 years  parrello  Converted to use new name for Contrain method.
Tracer.pl  1.1  10 years  parrello  New script used to route STDERR messages to the trace log.
TransactFeatures.pl  1.20  10 years  parrello  Removed obsolete use clause.
WebAppBackend.pl  1.2  9 years  jared  make user and org commands case insensitive
WikiMaker.pl  1.6  10 years  parrello  Added more trace messages.
accumulate_pegs_to_scenario_paths.pl  1.1  7 years  dejongh  determine which pegs in an organism are involved in which scenario paths
aclh.pl  1.11  10 years  paarmann  added new parameter to dump contribs
aclh_reload_contrib.pl  1.2  9 years  wilke  added db handle in ach call
add_assertions_of_function.pl  1.39  5 years  golsen  Add error report of invalid confidence value. Fix the parsing of roles into the ...
add_assignments.pl  1.3  12 years  olson  Add license words.
add_attributes_from_file.pl  1.1  11 years  redwards  just a simple attribute loader
add_close_genes.pl  1.2  12 years  olson  Add license words.
add_dlits.pl  1.1  7 years  parrello  New script for adding protein-based Dlits.
add_figbar_and_genome_attributes.pl  1.1  11 years  mkubal  v1
add_phage_from_rast.sh  1.1  5 years  redwards   a set of scripts for adding phage genomes to the seed
add_prots_to_tree.pl  1.1  11 years  golsen  New script for adding proteins to an existing tree.
add_rbs_data_for_start_predictions.pl  1.3  10 years  gdpusch  Added FIGV support. -- /gdp
add_sim_data_for_start_predictions.pl  1.8  10 years  gdpusch  Added FIGV support. -- /gdp
add_start_data_for_start_predictions.pl  1.4  10 years  gdpusch  Added FIGV support. -- /gdp
add_structured_english.pl  1.4  10 years  disz  Added escape arg to structured engkish
add_to_alignment.pl  1.8  7 years  golsen  Fix the libraries used for I/O.
add_to_subsystems.pl  1.1  12 years  overbeek  add add_to_subsystems
adjacent.pl  1.3  10 years  redwards  changing chop to chomp
ali_to_seq.pl  1.2  12 years  olson  Add license words.
ali_tree.pl  1.4  11 years  overbeek  add strip comments argument on function_of
alias2fig.pl  1.2  12 years  olson  Add license words.
aliases_of.pl  1.6  12 years  olson  Add license words.
align_fasta.pl  1.4  4 months  golsen  Add support for mafft.
align_seqs.pl  1.1  11 years  overbeek  add utilities for computing alignments
align_with_clustal.pl  1.8  12 years  olson  Add license words.
align_with_clustal_2.pl  1.4  11 years  golsen  Trivial format change.
alignment_to_html.pl  1.4  6 years  golsen  Add more flexible color by residue: -R ale | default | gde | none
all_bbhs.pl  1.16  11 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
all_subsystems.pl  1.2  12 years  olson  Add license words.
alter_tbl.pl  1.4  12 years  olson  Add license words.
analyze_kmer_assignments.pl  1.1  8 years  olson  new script to compare output of assign_using_kmers to current SEED assignments
analyze_loose_sets.pl  1.3  7 years  parrello  Added CSV output that can be used to generate a spreadsheet of recommended funct...
analyze_package_logs.pl  1.1  12 months  parrello  Changes copied from SEEDtk project.
analyze_scenario_connections.pl  1.4  10 years  dejongh  Changes to move the 'All' scenarios directory to FIG_Config::global/Models/All
annotate-ss-with-pattyfams.pl  1.1  2 years  olson  New scripts.
annotation_counts.pl  1.2  7 years  disz  Check in coming dates
apply_annotations.pl  1.7  4 years  olson  Fix in the case of an empty skiplist.
apply_automatic_subsystem_updates.pl  1.1  7 years  olson  Scripts to run rapid_subsystem_inference_batch across all genomes, and to apply ...
apply_map.pl  1.2  12 years  olson  Add license words.
apply_peg_changes_to_subsystem.pl  1.3  12 years  olson  Add license words.
are_close.pl  1.1  12 years  overbeek  fixes to extract_genomes
assemble_selected.pl  1.1  17 months  parrello  Changes copied from SEEDtk project.
assess_completeness.pl  1.9  10 years  gdpusch  Fixed leading-whitspace bug.
assess_gene_call_quality.pl  1.14  8 years  olson  don't write the overlap report to metadata log; it is very large.
assign.pl  1.2  12 years  olson  Add license words.
assign_figfam.pl  1.1  9 years  arodri7  add original assign_using_ff
assign_synonym_ids.pl  1.2  12 years  olson  Add license words.
assign_synonym_ids_to_nr.pl  1.2  12 years  olson  Add license words.
assign_synonym_ids_to_sims.pl  1.2  12 years  olson  Add license words.
assign_to_close_strains.pl  1.10  12 years  overbeek  fixes to Assignments.pm
assign_to_dna_using_kmers.pl  1.6  6 years  redwards  adding details to the assign to DNA for kmer calls
assign_to_hypo.pl  1.3  12 years  olson  Add license words.
assign_to_sets.pl  1.5  12 years  olson  Add license words.
assign_to_unchanged.pl  1.3  10 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
assign_towards_subsystems.pl  1.2  12 years  olson  Add license words.
assign_using_ff.pl  1.9  9 years  arodri7  commit changes
assign_using_ff_original.pl  1.1  9 years  arodri7  original format of assign_using_ff
assign_using_ff_parallel.pl  1.2  9 years  arodri7  made updates to functions used for updating FIGfams
assign_using_kmers.pl  1.8  8 years  olson  Add support for explicitly specifying FRI.db, setI.db, table.binary
assign_with_no_sims.pl  1.2  12 years  olson  Add license words.
assigned_functions_from_rast.pl  1.1  6 years  redwards  adding code to make an assigned_functions file in rast dirs
at.pl  1.3  7 years  fangfang  update
auto_assign.pl  1.19  10 years  olson  Add -orgdir option to use FIGV and its indexed sims.
backfill_gaps.pl  1.21  3 years  gdpusch  Accept as few as a single template if it is in a subsystem.
backup_critical_data.pl  1.5  9 years  olson  fix bug that kept subsystems from being backedup
backup_subsystems.pl  1.3  10 years  parrello  Fixed a POD error.
bayes_expected_start_scores.pl  1.3  11 years  overbeek  Added comments to expalin logic. -- gdp
bbh_synteny.pl  1.1  3 years  redwards  adding code to make syntentic plots
bbhs.pl  1.7  12 years  olson  Add license words.
best_hits.pl  1.2  12 years  olson  Add license words.
best_tree_using_proml_on_cluster.pl  1.1  11 years  overbeek  add best_tree_using_proml_on_cluster
bielefeld_tarfile_to_seed.pl  1.7  12 years  overbeek  Tweaked usage msg. -- /gdp
blast2gff.pl  1.23  8 years  redwards  adding an option for gziped files
blastP.pl  1.1  9 years  olson  Switch to using assign_functions_to_prot_set in assign_using_kmers.pl. Add blast...
blast_pdb_against_nr_on_tla.pl  1.1  11 years  mkubal  blast pdb against nr
blast_request.pl  1.2  12 years  olson  Add license words.
blastn_chunks.pl  1.3  11 years  overbeek  initial, undebugged version of edit_feature.cgi
blastn_seqs.pl  1.2  12 years  olson  Add license words.
blastp_pseq.pl  1.6  9 years  redwards  adding a default cutoff
blocked_by.pl  1.1  4 years  overbeek  find out why a kmer was blocked
boot_cluster_seed.pl  1.5  12 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
br_evaluate_properties.pl  1.1  5 years  overbeek  trying to commit a working copy
break_scaffolds.pl  1.2  12 years  olson  Add license words.
bring_system_up_to_date.pl  1.2  12 years  olson  Add license words.
bring_tree_up_to_ali.pl  1.5  11 years  overbeek  debugged version of bring_tree_up_to_ali
build_PGs_for_OTUs.pl  1.2  6 years  overbeek  fix path
build_SEED_nr.pl  1.1  8 months  olson  Add SEED NR builder using all_valid_protein_features_in_SEED
build_access_sets.pl  1.2  12 years  olson  Add license words.
build_alignments_for_subsystems.pl  1.4  12 years  olson  Add license words.
build_alignments_from_spreadsheet.pl  1.7  12 years  redwards  using is_environmental
build_aligns_and_trees_for_seqs.pl  1.2  6 years  fangfang  removed comments
build_all_prok_seqs.pl  1.1  8 years  overbeek  get all protein sequences for complete prokaryotic genomes
build_anno_clearinghouse.pl  1.6  10 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
build_contigs_blastdb.pl  1.1  2 years  olson  New blastdb builders.
build_dnaseq_blastdb.pl  1.1  2 years  olson  New blastdb builders.
build_dtr_distro.pl  1.4  7 years  devoid  Making changes to build distro to support ModelSEED packages. Modified Files: F...
build_excel_gene_table.pl  1.3  12 years  olson  Add license words.
build_exemplar_fasta.pl  1.3  12 years  olson  Add license words.
build_family_dir_from_genera.pl  1.3  3 weeks  olson  Checkpoint before viruses change.
build_figfam_pssm_db.pl  1.2  11 years  gdpusch  Major modifications to &load_family_ids()
build_initial_objects_for_start_predictions.pl  1.12  10 years  gdpusch  Modified to also work on new genomes using "FIGV.". -- /gdp
build_nap_alignments.pl  1.4  6 years  overbeek  place the PseudoGene alignments
build_new_figfam_release.pl  1.5  8 years  disz  FigFam 6 digit problem
build_nohit_fasta.pl  1.2  12 years  olson  Add license words.
build_nr.pl  1.22  10 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
build_nr_md5.pl  1.1  5 years  olson  md5 nr builder
build_nr_sources.pl  1.14  11 years  olson  Rollup of various rast-related changes.
build_partition_index.pl  1.1  10 years  overbeek  return empty list of failure to open FIFfam
build_prok_nonff_fasta.pl  1.4  8 years  disz  FigFam 6 digit problem
build_protein_families.pl  1.5  12 years  olson  Add license words.
build_sample_sigs.pl  1.1  3 weeks  parrello  Changes copied from SEEDtk project.
build_sas_distro.pl  1.11  7 years  devoid  Making changes to build distro to support ModelSEED packages. Modified Files: F...
build_sas_distro_from_cvs.pl  1.5  7 years  olson  Revert to the versions from backups.
build_sets_from_clusters.pl  1.2  7 years  parrello  Minor fixes for debugging.
build_solid_set.pl  1.3  5 years  overbeek  avoid including transport or regulatory clusters
build_syn.pl  1.2  12 years  olson  Add license words.
cache_comparison_data.pl  1.11  9 years  paczian  fixed load order of function files in RAST vs SEED organisms
call_coregulated_clusters_on_chromosome.pl  1.8  6 years  overbeek  reduce threshhold on pcc from 0.7 to 0.6
call_genes.pl  1.4  8 years  olson  fix ANNOserver args
call_genome_using_glimmer.pl  1.4  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
cat_spreadsheet.pl  1.2  12 years  olson  Add license words.
changed_starts.pl  1.7  12 years  olson  Add license words.
check_alignment.pl  1.2  12 years  olson  Add license words.
check_all_lost_sims.pl  1.2  12 years  olson  Add license words.
check_all_subsystems.pl  1.11  9 years  olson  Transform the single big select into a prepared statement on per-role select.s
check_and_extend_all_subsystems.pl  1.7  11 years  overbeek  fix call to rapid_subsystem_extension in check_and_extend_all_subsystems
check_changes_in_organisms.pl  1.2  12 years  olson  Add license words.
check_consistency_of_rectangles.pl  1.1  5 years  overbeek  check consistency of solid rectangles
check_consistency_of_sample.pl  1.7  9 years  redwards  correcting looping through parts of the genomes
check_fast_sims.pl  1.2  12 years  olson  Add license words.
check_fasta_for_dups.pl  1.1  11 years  olson  Missing scripts.
check_figfams.pl  1.6  10 years  olson  Introduct &FIG::get_figfams_data()
check_for_new_genomes.pl  1.3  9 years  overbeek  print stats as you go
check_for_possible_mobile_elements.pl  1.1  11 years  overbeek  add code to search for mobile elements
check_for_scenario_reachability.pl  1.3  10 years  dejongh  switch to scenario_directory
check_for_unique_sims.pl  1.2  12 years  olson  Add license words.
check_genomes_by_ribo_proteins.pl  1.2  5 years  overbeek  handle dup assignments
check_gto.pl  1.1  2 months  parrello  Changes copied from SEEDtk project.
check_hope_info.pl  1.8  8 years  dejongh  updates to check for invalid maps and reaction/ec mismatches
check_lost_sims.pl  1.2  12 years  olson  Add license words.
check_model.pl  1.7  10 years  dejongh  switch to scenario_directory
check_model_v2.pl  1.2  10 years  dejongh  switch to scenario_directory
check_nr_and_peg_synonyms.pl  1.2  12 years  olson  Add license words.
check_peg_assignments.pl  1.3  12 years  olson  Add license words.
check_peg_placement.pl  1.1  11 years  overbeek  redone FIGfam stuff
check_rast.pl  1.1  16 months  parrello  Changes copied from SEEDtk project.
check_sims_basic.pl  1.8  12 years  redwards  using is_environmental instead of seven 9s
check_sims_for_added_genome.pl  1.1  5 years  redwards   a set of scripts for adding phage genomes to the seed
check_sims_syntax.pl  1.3  12 years  olson  Add license words.
check_starts_for_peg_sets.pl  1.5  12 years  olson  Add license words.
check_starts_for_pegs.pl  1.5  12 years  olson  Add license words.
check_subs_and_split_warnings.pl  1.3  10 years  overbeek  minor fix to handle deleted subsystems
check_subsystems.pl  1.7  11 years  overbeek  strip comments on functions for subsystem checking
check_tbl.pl  1.2  12 years  olson  Add license words.
clean_bad_contigs.pl  1.2  11 months  parrello  Updates from SEEDtk
clean_sims.pl  1.2  12 years  olson  Add license words.
clean_subsystems.pl  1.2  12 years  olson  Add license words.
cleanup_figfams_updates.pl  1.1  9 years  arodri7  commit changes
close_connections.pl  1.2  11 years  overbeek  add strip comments argument on function_of
clustal2fasta.pl  1.2  12 years  olson  Add license words.
clustal_to_fasta.pl  1.2  12 years  olson  Add license words.
cluster_by_bbhs.pl  1.2  12 years  olson  Add license words.
cluster_by_sim.pl  1.2  12 years  olson  Add license words.
cluster_exp.pl  1.1  8 years  overbeek  cluster experiments into states
cluster_objects.pl  1.10  2 months  parrello  Changes copied from SEEDtk project.
clustered_hypotheticals.pl  1.2  8 years  overbeek  major rewrite
codon_counts_x_and_p.c  1.1  6 years  golsen  Support for codon usage analyses.
codon_freq_eval_2.c  1.1  6 years  golsen  Support for codon usage analyses.
collate_reads.pl  1.1  3 weeks  parrello  Changes copied from SEEDtk project.
collect_related_sequences.pl  1.3  11 years  golsen  Encapsulate all of the SEED-dependent functions in the perl module. It should st...
compareMR.pl  1.1  11 years  overbeek  basic stuff for comparing metabolic reconstructions
compare_annotation_sets.pl  1.1  4 years  olson  Annotation comparison tool.
compare_ec_gary_table.pl  1.1  3 years  redwards  module and scripts to compare EC numbers to what we have in the SEED
compare_figfam_release_results.pl  1.5  9 years  arodri7  commit changes
compare_gto_assigned_roles.pl  1.1  4 years  gdpusch  Initial checkin.
compare_gto_called_CDSs.pl  1.1  4 years  gdpusch  Initial checkin.
compare_scenarios.pl  1.5  10 years  dejongh  Changes to move the 'All' scenarios directory to FIG_Config::global/Models/All
compare_tbls.pl  1.5  12 years  overbeek  Minor change to output. -- /gdp
compare_tree_and_alignment.pl  1.2  12 years  olson  Add license words.
compare_two_sets_of_calls.pl  1.3  9 years  overbeek  stuff for gene calling
complement_fasta.c  1.1  6 years  golsen  Support for codon usage analyses.
complete_genomes.pl  1.7  12 years  olson  Add license words.
compute_CELLO_and_TMPRED.pl  1.2  11 years  mkubal  test for dir exist
compute_PCA_for_metagenomes.pl  1.1  9 years  mkubal  called by PCA_ssav
compute_PCA_with_metagenomes_as_variables.pl  1.1  9 years  mkubal  called by PCA_mgav
compute_PSEED_reconstructions.pl  1.2  7 years  olson  More fixups.
compute_atomic_regulons.pl  1.3  5 years  overbeek  compute correspondences for a pan genome
compute_atomic_regulons_for_dir.pl  1.2  7 years  overbeek  loosen threshhold of mismatches
compute_changed_ids_for_nrs.pl  1.5  9 years  olson  misc fixes
compute_contig_md5.pl  1.4  11 years  olson  rollup of metagenome server changes
compute_crc64_for_all_pegs.pl  1.1  11 years  mkubal  v1
compute_dbdir_checksum.pl  1.3  12 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
compute_ev_code_attributes.pl  1.2  10 years  overbeek  do not include cluster-based subsystems in forming evidence codes
compute_extra_dlit_data.pl  1.4  10 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
compute_fasta_lengths.pl  1.1  8 years  olson  Precompute fasta lengths for the non-FF nr.
compute_figfam_assignments.pl  1.2  8 years  olson  Clean up debugging, write concatenated output file.
compute_genome_counts.pl  1.25  9 years  olson  Fix bug where compute_genome_counts fails to run on a genome directory with mult...
compute_genome_similarity.pl  1.1  11 years  olson  Missing scripts.
compute_mw_and_pi.pl  1.2  11 years  mkubal  one genome at a time
compute_mw_and_pi_with_BioPerl.pl  1.1  11 years  mkubal  computes mw and pi for all pegs in complete genomes
compute_new_ids.pl  1.2  12 years  olson  Add license words.
compute_pc.pl  1.2  5 years  overbeek  compute correspondences for a pan genome
compute_pchs_from_sims.pl  1.2  11 years  olson  Rollup of changes for the new RAST install.
compute_pins.pl  1.4  10 years  olson  undo bogus commit
compute_pins_and_clusters.pl  1.2  12 years  olson  Add license words.
compute_potential_fusions.pl  1.12  12 years  overbeek  fix to fusions
compute_ribo_ratio.pl  1.1  5 years  overbeek  quality control using ribo proteins
compute_ribo_ratio_by_function.pl  1.1  5 years  overbeek  quality control using ribo proteins
compute_sim_chunk.pl  1.3  12 years  olson  add working-on-chunk support
compute_simple_scores.pl  1.4  12 years  olson  Add license words.
compute_stats_for_kmer_hits.pl  1.2  4 years  overbeek  handle a strange floating point issue
compute_translation_MD5.c  1.3  7 years  redwards  ignoring stops
condense_blast.pl  1.2  12 years  olson  Add license words.
condense_kmer_output.pl  1.2  4 years  overbeek  generalize to kbase
conditionally_assign.pl  1.6  6 years  golsen  Just a little more testing and nicer useage info.
connect_PDB_to_FIGfams.pl  1.1  10 years  arodri7  update changes
connect_PDB_to_FIGfams_worker.pl  1.1  10 years  arodri7  update changes
connections_between.pl  1.8  9 years  overbeek  fixes to making close strain data
convert-blast-to-m8.pl  1.1  9 years  olson  Convert full blast output to -m8 output using Gary's blast parsing code.
convert_tbl_files.pl  1.1  7 years  parrello  New script for fancy tbl file conversion.
core_PGF_stats.pl  1.1  20 months  jdavis  Adding core_PGF_stats.pl
corr_build_connections.pl  1.1  7 years  parrello  New stuff for Salmonella sets.
correct_frameshifts.pl  1.26  6 years  gdpusch  Grandfather in "-just_mark" in addition to "-justMark".
correct_gff_missing_contigs.pl  1.5  10 years  redwards  correcting a weird error
count_bases.pl  1.2  12 years  olson  Add license words.
crc64.py  1.1  10 years  mkubal  uses for mapping of interpro downlaod to pegs
create-new-page.pl  1.6  6 years  disz  added sopme more use lines
createTIGRfamSrc.pl  1.1  10 years  bartels  *** empty log message ***
create_ff_covering_skeleton.pl  1.3  6 years  overbeek  remove invocation of representative_sequences
create_sims_btree.pl  1.1  12 years  olson  BTREE-index versions of these. Experimental still.
cripple_gto.pl  1.2  2 months  parrello  Changes copied from SEEDtk project.
cs_adjacency_data.pl  1.6  3 years  overbeek  fix tmp on sort
curator_of.pl  1.1  12 years  overbeek  minor fixes to assignment for close strains
daily.pl  1.9  6 years  disz  new right side
das_test.pl  1.2  12 years  olson  Add license words.
db_xrefs_of.pl  1.4  12 years  olson  Add license words.
delete_all_attribute_files.pl  1.2  12 years  overbeek  RAE: New delete attribute files to remove all files. maybe this will work
delete_fids_from_orgdir.pl  1.2  22 months  gdpusch  Improved command-line argument processing
delete_functions_for_nonextent_ff.pl  1.1  5 years  overbeek  delete functions for nonexisting families
delete_genomes_from_sims.pl  1.2  12 years  olson  Add license words.
diff_tbls.pl  1.2  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
difference_between_two_databases.pl  1.1  9 years  redwards  code for generating the delta between two databases
direct_functional_coupling.pl  1.4  11 years  overbeek  tighten length constraints for figfam matching
display_tree.pl  1.4  12 years  olson  Add license words.
distribute_attributes.pl  1.11  12 years  olson  Add license words.
dna_seq.pl  1.2  12 years  olson  Add license words.
dose_response_extract.pl  1.2  3 weeks  parrello  Changes copied from SEEDtk project.
dose_response_ic50.pl  1.2  3 weeks  parrello  Changes copied from SEEDtk project.
dose_response_sheets.pl  1.2  3 weeks  parrello  Changes copied from SEEDtk project.
dp.pl  1.4  9 years  redwards  editing header info
dump_attributes.pl  1.2  12 years  olson  Add license words.
dump_machine_state.pl  1.3  12 years  olson  Add license words.
dump_ss_classification.pl  1.1  9 years  redwards  adding ss classification methods
duplicate_genomes.pl  1.1  5 years  redwards   a set of scripts for adding phage genomes to the seed
ec_compare_sib.pl  1.1  3 years  redwards  module and scripts to compare EC numbers to what we have in the SEED
embl2gff.pl  1.20  12 years  olson  Add license words.
embl2gff_addmd5.py  1.2  12 years  olson  Add license words.
ensure_genome_registration.pl  1.1  11 years  olson  generate feature registration stuff
estimated_fabric.pl  1.1  9 years  overbeek  code for processing fabrics and population estimates
ev_code_cron.pl  1.16  10 years  parrello  Updated comments to mention the replacement scripts.
eval_matrix.py  1.2  3 weeks  parrello  Changes copied from SEEDtk project.
evaluate_annotation_consistency.pl  1.1  5 years  fangfang  script for evaluating annotation consistency
evaluate_properties.pl  1.1  5 years  overbeek  a tool that uses boolean evaluation
evaluate_quality_of_trees.pl  1.4  11 years  overbeek  debugged version of bring_tree_up_to_ali
ex_add_conditions.pl  1.1  5 years  overbeek  add conditions/samples
ex_adjust_peg_on_off.pl  1.1  5 years  overbeek  expression pipeline + ato,ic regulons
ex_compute_pccs.pl  1.3  5 years  overbeek  add spearman stuff
ex_fillout_ar_data.pl  1.1  5 years  overbeek  added steps
ex_get_adjacency_based_estimates.pl  1.2  4 years  overbeek  minor changes
ex_get_subsystem_based_estimates.pl  1.2  4 years  overbeek  minor changes
ex_make_initial_atomic_regulons.pl  1.2  4 years  overbeek  two embarrassing bugs in same_profile
ex_make_on_off_calls.pl  1.3  5 years  overbeek  get locus/peg right
ex_pipeline_ross.pl  1.5  4 years  overbeek  added some documentation
ex_rare_ar_and_pegs.pl  1.1  5 years  overbeek  added steps
ex_set_on_off_for_atomic_regulons.pl  1.1  5 years  overbeek  expression pipeline + ato,ic regulons
ex_split_atomic_regulons.pl  1.3  4 years  overbeek  it is ok to have nonpeg aliases
exclude_genomes.pl  1.3  10 years  parrello  Fixed a POD error.
exec-cgi.pl  1.1  8 years  olson  cgi executor for mac rast
exp_pc_compute.pl  1.10  6 years  parrello  Updated to process directories in order.
expand_blast_table.pl  1.2  12 years  olson  Add license words.
expand_multifunctional_roles.pl  1.3  12 years  olson  Add license words.
expand_sims.pl  1.2  10 years  olson  *** empty log message ***
expand_transferred_chunks.pl  1.4  12 years  olson  Add license words.
explore_subsys_pmid.pl  1.5  11 years  hwang  PEG information is no longer stored in the file. Parsing of the file in this scr...
export_ACH_resolution_DB.pl  1.2  10 years  overbeek  fixes relating to comments
export_all_viruses.pl  1.1  5 years  redwards   a set of scripts for adding phage genomes to the seed
export_dlits.pl  1.2  10 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
export_genome_as_gff.pl  1.6  12 years  olson  Add license words.
export_phage_data.pl  1.4  5 years  redwards  a cron job to export phage data
export_similarity_request.pl  1.3  12 years  overbeek  minor fixes to assignment for close strains
export_subsystem.pl  1.1  2 years  olson  Subsystem exporter for NCBI.
export_subsystem_as_gff.pl  1.2  12 years  olson  Add license words.
extend_subsys.pl  1.7  12 years  redwards  using is_environmental instead of seven 9s
extend_subsystem.pl  1.2  12 years  olson  Add license words.
external_calls.pl  1.2  12 years  olson  Add license words.
extract_DNA_for_whole_ORFs.pl  1.4  9 years  gdpusch  Fixed possible DNA case sensitivity.
extract_DNA_sequence_from_object_for_start_predictions.pl  1.2  12 years  olson  Add license words.
extract_data_for_syncing_after_update.pl  1.6  12 years  olson  Add license words.
extract_data_to_keep.pl  1.5  12 years  olson  Add license words.
extract_fasta_idmap.pl  1.1  12 years  overbeek  RAE: Adding FigKernelScripts/extract_fasta_idmap.pl
extract_genes.pl  1.5  12 years  olson  Add license words.
extract_genomes.pl  1.38  12 years  overbeek  changes to support dynamic sims and updates
extract_genomes_from_samples.pl  1.2  5 years  overbeek  needs work on getting rRNAs
extract_halo_genomes.pl  1.7  5 years  overbeek  compute correspondences for a pan genome
extract_metagene_contigs.pl  1.12  8 years  gdpusch  Updated search for executables to revised software environment.
extract_sp_links.pl  1.3  12 years  olson  fix -h error
extract_subset_from_sprout_data.pl  1.2  12 years  olson  Add license words.
fabric_vec.pl  1.1  9 years  overbeek  add ability to make fabric vecs
fast_blastp.pl  1.1  10 years  overbeek  fast_blastp is a tool to support rapid similarity estimates using FIGfam partiti...
fast_grep.pl  1.1  5 years  overbeek  example of systead
fast_project.pl  1.3  2 years  olson  bugfix
fast_project_ref_to_GTO.pl  1.1  3 years  parrello  Changes copied from SEEDtk project.
fasta_cksum.c  1.4  12 years  olson  Doh, put proper comments in for C code.
fasta_dna.pl  1.1  2 months  parrello  Changes copied from SEEDtk project.
fasta_for_hypo.pl  1.2  12 years  olson  Add license words.
fasta_size.pl  1.1  9 years  overbeek  add fasta_size
fasta_to_phylip.pl  1.2  12 years  olson  Add license words.
fastasize.c  1.3  12 years  olson  Doh, put proper comments in for C code.
fc_figfams.pl  1.3  8 years  disz  FigFam 6 digit problem
feature_length_histogram.pl  1.4  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
features_with_role.pl  1.1  11 years  golsen  Function to get the ids or sequences of features that match a given role. Uses F...
fetch_models_for_genomes.pl  1.1  7 years  fangfang  initial import
fetch_seed_gto.pl  1.4  3 years  parrello  Changes copied from SEEDtk project.
ff.pl  1.7  8 years  disz  FigFam 6 digit problem
fid2dna.pl  1.2  12 years  olson  Add license words.
fig.pl  1.157  3 years  overbeek  add change_funcrole
fig_net.pl  1.4  10 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
fig_rpc.pl  1.4  10 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
fig_specific_sequences.pl  1.3  12 years  redwards  using is_environmental instead of seven 9s
fig_xmlrpc_server.pl  1.5  12 years  olson  Add license words.
figfam.pl  1.23  8 years  disz  FigFam 6 digit problem
figfam_quality_control.pl  1.8  9 years  arodri7  commit changes
figfam_size_distribution.pl  1.1  10 years  arodri7  update changes
figfam_subsystems.pl  1.2  9 years  arodri7  commit changes
fill_in_cell.pl  1.2  12 years  olson  Add license words.
fill_in_roles.pl  1.4  12 years  olson  Add license words.
fill_subsys.pl  1.5  12 years  olson  Add license words.
filter_and_merge_gene_sets.pl  1.2  7 years  overbeek  merge is better
filter_codon_counts.pl  1.1  6 years  golsen  Support for codon usage analyses.
filter_figfams.pl  1.2  11 years  overbeek  add computation of alignments to building FIGFAMS
filter_new_overlaps.pl  1.2  12 years  olson  Add license words.
filter_on_known.pl  1.1  8 years  overbeek  filter pegs with no raw data
filter_overlaps.pl  1.5  12 years  overbeek  Added some more diagnosting lines. -- /gdp
filter_pegs_in_subsystems.pl  1.4  12 years  olson  Add license words.
filter_tbl_overlaps.pl  1.10  12 years  overbeek  set up find_neighbors to handle existing genomes
filter_trunc_and_fs.pl  1.2  8 years  olson  Add SeedUtils::map_to_families for iterating over families.2c files. Make filte...
find_IS.pl  1.8  4 years  olson  add sas tag
find_RNA_genes.pl  1.1  3 years  golsen  Make blast+ the default in find_nucleotide_homologs, solving an issue with occas...
find_SEED_SSU_rRNA_genes.pl  1.7  5 years  golsen  Update the reference RNA module name.
find_approx_neigh.pl  1.8  5 weeks  gdpusch  Conversions from SAPserver FIGfams to direct FIG.pm access to PATtyFams. (Remove...
find_bad_conflicts.pl  1.1  12 years  overbeek  fixes to wseekly statistics
find_bad_contigs.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
find_bidir_best_hits.pl  1.1  4 years  fangfang  import Gary's find_bidir_best_hits script
find_close_genomes.pl  1.2  2 years  parrello  Changes copied from SEEDtk project.
find_essential_reactions.pl  1.3  10 years  dejongh  switch to scenario_directory
find_gaps.pl  1.9  9 years  gdpusch  Fixed (hopefully) incorrectly handled out-of-bounds cases.
find_genes_based_on_kmers.pl  1.9  7 years  olson  More fixups.
find_genes_based_on_neighbors.pl  1.24  9 years  olson  Switch to FFs and FF instead of FigFams and FigFam
find_genes_based_on_neighbors_par.pl  1.1  8 years  olson  parallel version of find_genes_based_on_neighbors
find_genes_in_families.pl  1.22  9 years  olson  Switch to FFs and FF instead of FigFams and FigFam
find_maximal_clusters.pl  1.2  12 years  olson  Add license words.
find_miscalled_genes.pl  1.5  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
find_missing_genes.pl  1.10  8 years  olson  more RAST fixes (some of these may need to be backported to use the SAP version ...
find_missing_lib_inputs.pl  1.6  10 years  dejongh  switch to scenario_directory
find_missing_lib_inputs_v2.pl  1.2  10 years  dejongh  switch to scenario_directory
find_model_cofactors.pl  1.7  10 years  dejongh  switch to scenario_directory
find_model_information.pl  1.7  10 years  dejongh  switch to scenario_directory
find_model_information_v2.pl  1.2  10 years  dejongh  switch to scenario_directory
find_more_instances_for_veronika.pl  1.1  6 years  overbeek  Fangfang tools to support Veronika
find_neighbors.pl  1.39  8 years  disz  FigFam 6 digit problem
find_neighbors_by_sim.pl  1.4  10 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
find_neighbors_using_figfams.pl  1.11  9 years  olson  Switch to FFs and FF instead of FigFams and FigFam
find_new_annotations.pl  1.6  5 years  parrello  Fixed to recover from genomes with missing annotation files.
find_poss_errs.pl  1.3  8 years  disz  FigFam 6 digit problem
find_poss_fs.pl  1.1  10 years  overbeek  add code to fix frameshifts in a genome
find_protein_homologs.pl  1.2  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
find_rnas.pl  1.2  8 years  olson  fix ANNOserver args
find_selenoproteins.pl  1.4  10 years  golsen  Add functions to reference selenoproteins, and add change the set slightly. Rep...
find_special_proteins.pl  1.4  10 years  gdpusch  Suppress writing "called_by" and "special_pegs" when "-keep" is selected. -- /gd...
find_subsys.pl  1.3  10 years  overbeek  allow loose matching in rapid_propagation
fix_annotations.pl  1.2  12 years  olson  Add license words.
fix_eol.pl  1.2  12 years  olson  Add license words.
fix_ext_funcs.pl  1.2  12 years  olson  Add license words.
fix_invalid_fasta.pl  1.1  11 years  redwards  Initial release of programs to check and fix valid fasta format
flatten_attribute_files.pl  1.2  7 years  redwards  working on all subdirectories, not just a set of them
flatten_erdb_xml.pl  1.1  6 years  olson  script to write tabular form of ERDB XML file
flatten_fasta.pl  1.1  12 years  overbeek  add some minor utilities to flatten/unflatten fasta files
flattened_to_fasta.pl  1.1  12 years  overbeek  add some minor utilities to flatten/unflatten fasta files
flip_sims.pl  1.7  11 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
form_clusters.pl  1.2  9 years  parrello  Final Server updates.
format_partition_dbs.pl  1.2  9 years  overbeek  try
format_peg_dbs.pl  1.3  12 years  olson  Add license words.
fq_to_fa.pl  1.1  17 months  parrello  Changes copied from SEEDtk project.
freqs_2_dists.pl  1.1  6 years  golsen  Compute pairwise distances between sets of codon usage frequencies.
freqs_2_nj_tree.pl  1.3  6 years  golsen  Some minor changes.
function_of.pl  1.5  10 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
functionally_coupled.pl  1.7  10 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
fusion_of.pl  1.2  12 years  olson  Add license words.
gather_attributes.pl  1.8  12 years  olson  Add license words.
gather_genome_info.pl  1.2  9 years  olson  Add more data gathering
gather_pg_sets.pl  1.3  7 years  overbeek  minor fixes
gd_tree.pl  1.1  9 years  golsen  Add a command line program to make a png graphic from a newick tree file.
genbank2fasta.pl  1.2  9 years  redwards  correcting ORIGIN regexp
genbank2gff3.pl  1.5  12 years  olson  Add license words.
generate_GO_attributes.pl  1.1  11 years  overbeek  add GO attribute genertation
generate_GenomeGroups_for_sprout.pl  1.3  12 years  olson  Add license words.
generate_Property_for_sprout.pl  1.6  12 years  olson  Add license words.
generate_Source_for_sprout.pl  1.2  12 years  olson  Add license words.
generate_clusters.pl  1.1  5 years  overbeek  program to generate clusters for a reference genome by checking decay rates
generate_comparisons.pl  1.1  9 years  overbeek  stuff for gene calling
generate_dlit_ev_codes.pl  1.5  10 years  overbeek  switching to new ilidt/dlit stuff
generate_gene_blocks.pl  1.3  12 years  olson  Add license words.
generate_genome_feature_tables_for_sprout.pl  1.16  12 years  olson  Add license words.
generate_ilit_ev_codes.pl  1.4  10 years  overbeek  code relating to dlit/ilit maintenance
generate_ilits.pl  1.3  8 years  olson  fix for FFs changes
generate_input_for_auto_assignments.pl  1.2  12 years  olson  Add license words.
generate_intergenic_blocks.pl  1.3  12 years  olson  Add license words.
generate_kernel_css.pl  1.5  12 years  olson  Add license words.
generate_kmer_peg_rel.pl  1.1  4 years  olson  Initial commit of Ross kmer compare regions code, coped from ~overbeek/Ross/Gene...
generate_max_clusters.pl  1.2  12 years  olson  Add license words.
generate_partitionsP.pl  1.6  8 years  disz  FigFam 6 digit problem
generate_partitions_worker.pl  1.4  8 years  disz  FigFam 6 digit problem
generate_picked.pl  1.1  9 years  overbeek  stuff for gene calling
generate_pin_caches.pl  1.5  12 years  olson  Add license words.
generate_pinned_homologs.pl  1.2  12 years  olson  Add license words.
generate_prolog_facts.pl  1.6  6 years  overbeek  no fields with tabs
generate_similarities.pl  1.3  10 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
generate_sprout_links.pl  1.2  12 years  olson  Add license words.
generate_subsys_tables_for_sprout.pl  1.8  12 years  olson  Add license words.
genome_peg_dna.pl  1.3  11 years  golsen  Extensive modifications to allow more options, and handle large genomes by not r...
genome_set.t  1.1  4 years  olson  Genome set tests & database initialization script
genomes_of.pl  1.2  12 years  olson  Add license words.
genomes_with_essentiality_data.pl  1.1  12 years  redwards  Adding tools to handle essentiality data for Sveta
get_FIGfams_SS_NMPDR_stats.pl  1.1  9 years  arodri7  *** empty log message ***
get_NCBI_genome_attributes.pl  1.1  10 years  arodri7  get_NCBI_genome_attributes searches the NCBI internet sites for genome attribute...
get_ON_probes.pl  1.5  3 years  jdavis  updated joses new functional roles
get_PATRIC_AMR_data.pl  1.1  3 years  jdavis  adding get_PATRIC_AMR_data.pl
get_PATRIC_AMR_genome_list.pl  1.1  3 years  jdavis  adding get_PATRIC_AMR_genome_list.pl
get_PSEED_assignment_updates.pl  1.6  4 years  olson  Specialty protein & PATRIC caller code.
get_all.pl  1.2  5 years  disz  Fixed the example
get_all_annotations.pl  1.1  6 years  disz  New scripts to load the function audit trail database
get_all_dlits.pl  1.2  6 years  golsen  Fix some off by one errors.
get_best_set_of_genes_for_column.pl  1.3  12 years  olson  Add license words.
get_class_examples.pl  1.2  12 years  olson  Add license words.
get_close_pegs.pl  1.1  4 years  olson  Initial commit of Ross kmer compare regions code, coped from ~overbeek/Ross/Gene...
get_close_pegs_kmer_memcache.pl  1.2  4 years  olson  put hash size back appropriately
get_core_PGFs.pl  1.1  20 months  jdavis  Adding get_core_PGFs.pl
get_coupling_values.pl  1.3  8 years  overbeek  get rid of extraneous routine
get_dlit_data.pl  1.1  5 years  overbeek  exemplar code
get_dna.pl  1.6  10 years  gdpusch  Minor cosmetic change. -- /gdp
get_empty_ecs  1.3  12 years  olson  Add license words.
get_empty_ecs.pl  1.4  12 years  olson  Add license words.
get_ev_codes.pl  1.15  10 years  parrello  Updated comments to mention the replacement scripts.
get_evaluation_check.pl  1.3  11 years  bartels  added option -a for showing pegs that do not match via blast
get_evaluation_check_rast_new_vs_old.pl  1.1  11 years  bartels   compare old rast with development version
get_exemplars_as_needed.pl  1.3  5 years  overbeek  minor fixes
get_fam_corr.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
get_fam_rel.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
get_families.pl  1.14  4 years  olson  Clean up tempdir.
get_families_1.pl  1.9  4 years  overbeek  handle bars in genome ids
get_families_2.pl  1.4  4 years  olson  Add tempdir()/tempfile() calls to manage create temps in right place. Add status...
get_families_3.pl  1.3  4 years  overbeek  fixed documentation
get_families_4.pl  1.9  4 years  olson  Add tempdir()/tempfile() calls to manage create temps in right place. Add status...
get_families_final.pl  1.3  4 years  overbeek  fixed documentation
get_families_kmcl.pl  1.1  18 months  olson  KMCL processing.
get_fasta_for_tbl_entries.pl  1.11  9 years  gdpusch  Modified to remove complaints about uninitialed values when TBL entry does not c...
get_figfam_funcs.pl  1.1  12 years  overbeek  add install_anticipated_functions and some FIGfam tracking stuff
get_genome_object_from_seed.pl  1.3  3 years  olson  add pseed
get_genomes_from_ncbi.pl  1.1  9 years  wilke  *** empty log message ***
get_id_mapping_for_list_of_IDs.pl  1.1  10 years  wilke  Draft version for id mapping
get_journals_for_frole.pl  1.1  11 years  hwang  Files to get journal information from PubMed
get_journals_for_org.pl  1.1  11 years  hwang  this script is the backend to get journals using taxonomy id or name. This calls...
get_list_of_genomes_to_delete.pl  1.3  5 years  overbeek  more stringent bounds
get_long_enough.pl  1.2  12 years  olson  Add license words.
get_merged_families_2.pl  1.1  3 years  olson  Global merge code.
get_merged_families_3.pl  1.1  3 years  olson  Global merge code.
get_needed_corr.pl  1.1  6 years  overbeek  for veronika projections
get_neighbors_and_corr_to_ref.pl  1.7  8 years  olson  remove cat and shell usage.
get_nr_entries_without_sims.pl  1.4  12 years  olson  Add license words.
get_pairs.pl  1.1  9 years  parrello  New script to find certain functional roles close together.
get_pathways_for_EC.pl  1.2  12 years  olson  Add license words.
get_peg_md5_func_subsystem.pl  1.1  6 years  overbeek  to support assigning FigFam functions
get_potential_starts_for_start_predictions.pl  1.3  10 years  gdpusch  Added FIGV support. -- /gdp
get_pubmed_journals.pl  1.5  11 years  hwang  update comment that this is for peg curation
get_recent_annotations.pl  1.1  6 years  overbeek  to support assigning FigFam functions
get_rid_of_small_or_too_many_per_FF.pl  1.2  5 years  overbeek  allow short prots in subsys
get_rna_features_for_calling_genes.pl  1.2  9 years  overbeek  get rid of proteins
get_sims_for_start_predictions.pl  1.5  10 years  gdpusch  Added FIGV support. -- /gdp
get_ss_connections.pl  1.12  9 years  redwards  only call if not in a ss
get_subsystem_properties.pl  1.1  11 years  overbeek  minor modifications to get subsystems statistics
get_synonyms_from_ach_for_id.pl  1.2  10 years  wilke  *** empty log message ***
get_taxid_journals.pl  1.1  11 years  hwang  get journals from PMC using taxide
get_translations.pl  1.3  12 years  overbeek  get_translations can take PEG ids from STDIN
get_translations_for_genomes.pl  1.1  4 years  overbeek  get translations for a set of genomes
get_unique_kmers_for_rnaseq.pl  1.3  5 years  overbeek  take in K as a n argument
gff2Ontology.pl  1.4  12 years  olson  Add license words.
gff2ncbitab.pl  1.3  10 years  olson  add swissprot
gff2seed.pl  1.29  9 years  redwards  removing check for refseq ids
gff2tab.pl  1.5  11 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
gff_statistics.pl  1.1  11 years  redwards  releasing gff statistics
gi2fig.pl  1.3  12 years  olson  Add license words.
gjocodonlib.c  1.1  6 years  golsen  Support for codon usage analyses.
gjocodonlib.h  1.1  6 years  golsen  Support for codon usage analyses.
gjoseqio.c  1.1  6 years  golsen  Support for codon usage analyses.
gjoseqio.h  1.1  6 years  golsen  Support for codon usage analyses.
gjoseqlib.c  1.1  6 years  golsen  Support for codon usage analyses.
gjoseqlib.h  1.1  6 years  golsen  Support for codon usage analyses.
glue_tbl_to_metabolic_reconstruction.pl  1.1  8 years  olson  more anno server fixes, add some missing files
gset-initdb.pl  1.1  4 years  olson  Genome set tests & database initialization script
gto_complete_check.pl  1.1  20 months  parrello  Changes copied from SEEDtk project.
gto_crisprs.pl  1.1  16 months  parrello  Changes copied from SEEDtk project.
gto_to_tbl.pl  1.2  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
harvest_genomes_from_samples.pl  1.1  5 years  overbeek  possibly buggy - salvaged after the fact
html_parser.py  1.2  12 years  olson  Add license words.
ic50_compare.pl  1.1  3 weeks  parrello  Changes copied from SEEDtk project.
ic50_extract.pl  1.1  2 months  parrello  Changes copied from SEEDtk project.
identify_organism.pl  1.2  8 years  olson  changes for new server stuff
iedb.pl  1.10  12 years  overbeek  RAE: bugger, correcting the array dereferencing
import_external_sequences_step1.pl  1.8  12 years  olson  Add license words.
import_external_sequences_step3.pl  1.5  12 years  olson  Add license words.
import_similarity_bundle.pl  1.3  10 years  parrello  Fixed a POD error.
import_subsystems.pl  1.22  12 years  olson  Add license words.
index-pegsyn.pl  1.1  11 years  olson  Missing scripts.
index-pegsyn2.pl  1.1  10 years  olson  new version of pegsyn indexer that presorts data before inserting into the btree...
index_anno_clearinghouse.pl  1.3  11 years  olson  multiple id support, build fixes
index_annotations.pl  1.11  11 years  olson  bugfix
index_contig_files.c  1.5  12 years  olson  fix to work on 64-bit linux
index_contigs.pl  1.12  7 years  redwards  not reopening a file twice!
index_fasta.pl  1.2  12 years  olson  Add license words.
index_feature_dir_fasta.pl  1.1  10 years  olson  Index scripts for FIGV accleration.
index_figv_annos.pl  1.1  10 years  olson  Index scripts for FIGV accleration.
index_genome.pl  1.1  7 years  olson  Add index_genome.pl that will create the SEED data structures for a new SEED dir...
index_neighborhoods.pl  1.3  12 years  olson  Add license words.
index_nr.pl  1.2  11 years  olson  compute length btree also
index_pins.pl  1.3  12 years  olson  new pin indexer
index_sims.pl  1.12  9 years  olson  Bump id size.
index_sims_file.c  1.8  3 years  seaver  Fixed buffer overflow in index_sims_file that prevented the indexing of a larger...
index_sprout.pl  1.12  12 years  olson  Add license words.
index_subsystems.pl  1.15  7 years  olson  add nonaux role index
index_translation_files.c  1.8  7 years  redwards  ignoring stops
index_translations.pl  1.24  8 years  olson  Add index on fileno.
index_translations_MD5.pl  1.4  9 years  olson  revert changes
indirect_functional_coupling.pl  1.5  12 years  overbeek  indirect functional coupling should not be from a PEG to itself
indirect_functional_coupling_mcauliffe.pl  1.5  12 years  overbeek  indirect functional coupling should not be from a PEG to itself
init_FIG.pl  1.13  7 years  olson  fixes for when dbhost is set
init_dbserver.pl  1.3  12 years  olson  Add license words.
init_maps.pl  1.3  12 years  olson  Add license words.
init_peg_job_scheduler.pl  1.4  12 years  olson  Add license words.
initial_set.pl  1.2  12 years  olson  Add license words.
initialize_alignments_for_subsystems.pl  1.2  12 years  overbeek  fixes to extract_genomes, salvage_subsystem_rows and initialize_alignments_for_s...
initialize_ann_and_ev.pl  1.4  7 years  olson  fix typo
initialize_figfams.pl  1.12  8 years  disz  FigFam 6 digit problem
insert.pl  1.2  12 years  olson  Add license words.
insert_all.pl  1.2  12 years  olson  Add license words.
insert_into_a_tree.pl  1.5  11 years  overbeek  add tree_neighbors and latest phylogeny stuff
insert_prot_into_tree.pl  1.14  11 years  golsen  Continuing the update of tree packages and programs
install-data.pl  1.8  10 years  olson  fix to dvd data installer
install_annotations.pl  1.4  12 years  olson  Add license words.
install_anticipated_functions.pl  1.3  10 years  olson  Introduct &FIG::get_figfams_data()
install_assignments.pl  1.7  12 years  olson  Add license words.
install_code.pl  1.2  12 years  olson  Add license words.
install_feature_updates.pl  1.2  12 years  olson  Add license words.
install_features_batch.pl  1.1  10 years  olson  Add new script to install a batch of genomid.tbl / genomeid.fasta files. Initial...
install_lightweight_code.pl  1.2  12 years  olson  Add license words.
install_new_coupling_data.pl  1.3  11 years  olson  add option to install from a jobdir
install_partition_reps.pl  1.2  9 years  arodri7  commit change
install_partitions.pl  1.5  8 years  disz  FigFam 6 digit problem
install_rast_batch.pl  1.4  11 years  olson  more fixes
install_subsystems.pl  1.2  12 years  olson  Add license words.
install_translation_rules.pl  1.3  12 years  olson  Add license words.
interval.pl  1.2  12 years  olson  Add license words.
is_archaeal.pl  1.2  12 years  olson  Add license words.
is_bacterial.pl  1.2  12 years  olson  Add license words.
is_eukaryotic.pl  1.2  12 years  olson  Add license words.
is_prokaryotic.pl  1.2  12 years  olson  Add license words.
jgi_data_merge.pl  1.2  7 years  golsen  Fix the taxonomy to use NCBI full taxonomy if TAXONOMY does not exist.
just_inconsistent_sets.pl  1.1  7 years  overbeek  show inconsistyent sets
k-class-PSEED-kc.pl  1.1  3 years  jdavis  k-class-PSEED-kc.pl is a program to create a directory of kmer count files from ...
k-class-adaboost-classify.pl  1.1  3 years  jdavis  adding k-class-adaboost-classify.pl
k-class-adaboost-matrix-parallel.pl  1.1  3 years  jdavis  adding k-class-adaboost-matrix-parallel.pl
k-class-adaboost.pl  1.2  3 years  olson  Bob hacks to Jim's code
k-class-get-adaboost-tree-tips.pl  1.1  3 years  jdavis  adding k-class-get-adaboost-tree-tips.pl
k-class-get-bork-universals.pl  1.1  3 years  jdavis  This gets a set of universal proteins for a genome using blast
k-class-kc.pl  1.1  3 years  jdavis  Adding k-class-kc.pl, a wrapper of Fangfangs kc.pl code which runs kmc
k-class-representative_n_tree_tips.pl  1.1  3 years  jdavis  adding k-class-representative_n_tree_tips.pl
k-class-tree-from-contig-dir.pl  1.2  3 years  jdavis  had to strip .pl file extensions in system calls
keep_good_connections.pl  1.3  5 years  overbeek  change definition of required ratio
keep_only.pl  1.2  12 years  olson  Add license words.
km_build_Data.pl  1.20  2 years  olson  Commit updates to kmer build code.
km_build_function_index.pl  1.1  5 years  overbeek  Release 1.0: see ~overbeek/Ross/LoosenedKmers/bin/Release1.0/bin
km_build_just_otu_index.pl  1.1  5 years  overbeek  Release 1.0: see ~overbeek/Ross/LoosenedKmers/bin/Release1.0/bin
km_build_kmers_part1.pl  1.2  5 years  overbeek  fix test for fI
km_build_kmers_part2.pl  1.1  5 years  overbeek  Release 1.0: see ~overbeek/Ross/LoosenedKmers/bin/Release1.0/bin
km_pick_best_hit_in_peg.pl  1.4  2 years  olson  Some readability / documentation changes.
km_process_hits_to_regions.pl  1.6  19 months  olson  Fix accumulation of weighted score bug.
kmc  1.1  3 years  jdavis  adding kmc
kmer_classifier.pl  1.1  4 years  olson  Add Ross/Jim Davis kmer classifier code.
kmer_guts_net.pl  1.2  2 years  olson  Add sas tag.
kmer_property_search.pl  1.3  5 years  overbeek  make frac hits for kmer a parameter
kmer_search.pl  1.26  23 months  olson  Add debug flag
kp_build_Data.pl  1.5  5 years  overbeek  handle frac better
kp_get_properties_next_round.pl  1.1  5 years  overbeek  a little script to make next properties file in iterative training
kp_process_dna_hits.pl  1.4  4 years  olson  Fix regex bug.
kp_process_hits.pl  1.7  4 years  olson  Fix regex bug.
kp_run_tests.pl  1.5  4 years  overbeek  fix pubseed flag
label_all_nodes.pl  1.2  5 years  overbeek  unlabel/label
lengths_of_contigs.pl  1.2  12 years  olson  Add license words.
list_genomes.pl  1.2  12 years  olson  Add license words.
load_ACH_resolution_DB.pl  1.4  10 years  overbeek  fixes to quotemeta characters in loading comments
load_abstract_coupling.pl  1.3  12 years  parrello  Changed to use a single-character delimiter (for compatability with PostGRES).
load_atomic_regulons.pl  1.1  7 years  olson  initial atomic regulon table loader
load_attributes.pl  1.46  7 years  redwards  changing the attribute of the genome table
load_bbhs.pl  1.15  10 years  olson  *** empty log message ***
load_bbhs_btree.pl  1.1  12 years  olson  BTREE-index versions of these. Experimental still.
load_chromosomal_clusters.pl  1.2  12 years  olson  Add license words.
load_close.pl  1.9  11 years  overbeek  tighten length constraints for figfam matching
load_coupling.pl  1.9  12 years  olson  Remove debugging.
load_coupling_btree.pl  1.1  12 years  olson  BTREE-index versions of these. Experimental still.
load_distances.pl  1.5  12 years  olson  Add license words.
load_dlits.pl  1.5  10 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
load_ec_names.pl  1.6  9 years  olson  support for change in format to the KEGG/ECtable.
load_external_orgs.pl  1.3  12 years  olson  Add license words.
load_features.pl  1.24  10 years  olson  fix tmp file name.
load_function_transition_table.pl  1.1  6 years  disz  New scripts to load the function audit trail database
load_go.pl  1.2  11 years  overbeek  put in the fr2go stuff
load_hugo.pl  1.6  12 years  olson  Add license words.
load_id_correspondence.pl  1.3  10 years  olson  updates to the load_id_correspondence loader and searching code.
load_kegg.pl  1.15  8 years  dejongh  Fix KEGG location
load_kmer_peg_db.pl  1.1  4 years  olson  Initial commit of Ross kmer compare regions code, coped from ~overbeek/Ross/Gene...
load_kmers_into_memcache.pl  1.2  4 years  olson  memcache kmers code
load_links.pl  1.7  10 years  olson  Only load links from files ending in "links" (rather than files with it anywhere...
load_literature.pl  1.3  12 years  olson  Add license words.
load_local_maps.pl  1.3  12 years  olson  Add license words.
load_locks.pl  1.1  12 years  overbeek  introduce locks on features to block assignments
load_md5_alignment.pl  1.1  7 years  parrello  New script to load alignments into the PUBSEED server.
load_patric_map.pl  1.1  5 years  olson  Load patric mapping data.
load_pattyfams.pl  1.1  2 years  olson  pattyfam compute.
load_pch_pins.pl  1.2  12 years  olson  Add license words.
load_peg_mapping.pl  1.12  7 years  olson  Caching / FCGI speedup modifications.
load_pirsf.pl  1.14  12 years  overbeek  RAE: correcting load_pirsf not recognizing a firewall
load_propagation_locks.pl  1.1  5 years  olson  Initialize propagation locks table.
load_protein_families.pl  1.9  12 years  overbeek  RAE: extending protein families
load_sets.pl  1.5  12 years  olson  Add license words.
load_sims.pl  1.10  12 years  olson  If we are loading unmapped files (as generated by make_close -no-map and make_s...
load_ss_classification.pl  1.1  9 years  redwards  adding ss classification methods
load_wikipedia.pl  1.1  9 years  olson  Wikipedia cache loader.
location_of.pl  1.2  12 years  olson  Add license words.
ma_pipeline.pl  1.15  8 years  overbeek  get rid of RMA Key
ma_pipeline_ecoli.pl  1.3  5 years  overbeek  compute correspondences for a pan genome
ma_pipeline_shewanella.pl  1.6  8 years  overbeek  fixes to pipeline
macapp_files_to_genome_dir.pl  1.2  8 years  olson  Banish cp.
maint-remove-obsolete-aliases.pl  1.1  11 years  olson  Missing scripts.
make_CDD_attributes.pl  1.2  11 years  mkubal  fix to score format
make_CELLO_and_TMPRED_attributes.pl  1.2  11 years  mkubal  changed ; to :: for key separator
make_FigFamsData.pl  1.4  12 years  overbeek  order generated FIGfams
make_IPR_PFAM_GO_attributes.pl  1.3  11 years  mkubal  fix to score format
make_MFA_tool_input.pl  1.2  10 years  dejongh  switch to scenario_directory
make_MPS_model.pl  1.7  10 years  dejongh  switch to scenario_directory
make_MPS_model_v2.pl  1.2  10 years  dejongh  switch to scenario_directory
make_Ontology_database.pl  1.3  10 years  mkubal  provides usage when no argument given
make_PATRICfams.pl  1.4  6 years  overbeek  minor fix
make_PATRICfams_collapse_md5.pl  1.2  6 years  overbeek  minor fixes
make_PDB_attributes.pl  1.2  11 years  mkubal  fix to score format
make_PFAM_HMM_derived_attributes.pl  1.2  11 years  mkubal  added date as 2nd argument
make_PG.pl  1.3  7 years  overbeek  clarify condition
make_PHOBs_for_subsystems.pl  1.5  12 years  olson  Add license words.
make_PROSITE_PIR_PRODOM_attributes.pl  1.3  11 years  mkubal  fix to score format
make_Phobius_attributes.pl  1.2  11 years  mkubal  added date as 2nd argument
make_SBML_model.pl  1.6  10 years  dejongh  switch to scenario_directory
make_SignalP_attributes.pl  1.2  11 years  mkubal  changed ; to :: for key separator
make_annotations_for_sprout.pl  1.12  12 years  olson  Add license words.
make_assertions_from_uploads.pl  1.3  10 years  overbeek  get rid of debugging message
make_assignments_fit_initial_css.pl  1.4  12 years  olson  Add license words.
make_assignments_set.pl  1.3  12 years  olson  Add license words.
make_attribute_index.pl  1.6  12 years  olson  Add license words.
make_binary.pl  1.2  12 years  olson  Add license words.
make_calls.pl  1.4  12 years  olson  Add license words.
make_calls_for_start_predictions.pl  1.4  10 years  gdpusch  Added FIGV support. -- /gdp
make_cdd_ontology.pl  1.3  10 years  mkubal  provides usage when no argument given
make_close.pl  1.7  12 years  parrello  Fixed obsolete form of boundaries_of.
make_close_strain_data.pl  1.14  9 years  overbeek  fixes to making close strain data
make_close_strain_family_tabs.pl  1.2  12 years  overbeek  fixes to wseekly statistics
make_coreg_conjectures_based_on_subsys.pl  1.6  7 years  overbeek  allow working from estiomates of SS
make_external_sequence_data.pl  1.2  11 years  olson  remove .pl from invocations
make_fam_tabs.pl  1.5  12 years  overbeek  RAE: Protein Families interface and construction
make_fasta_btree.pl  1.1  11 years  olson  Utility for creating btree access for fasta files.
make_fig_files.pl  1.3  12 years  olson  Add license words.
make_figfam_tree.pl  1.2  8 years  disz  FigFam 6 digit problem
make_figfam_tree_worker.pl  1.2  8 years  disz  FigFam 6 digit problem
make_figfams.pl  1.3  12 years  overbeek  families.2c should get current function - not family function
make_genome_dir_for_close.pl  1.11  2 years  gdpusch  second tweak to avoid $contig=0 errors.
make_go_ontology.pl  1.3  10 years  mkubal  provides usage when no argument given
make_indexes.pl  1.18  6 years  golsen  Fixed bugs that made script crash with older SEED layout.
make_initial_partition_scores.pl  1.1  9 years  overbeek  additions to support partitioning of sims
make_interpro_ontology.pl  1.3  10 years  mkubal  provides usage when no argument given
make_jpg.pl  1.2  12 years  olson  Add license words.
make_kb_md5.pl  1.1  3 years  disz  New script to create kbstyle md5's
make_kegg_files.pl  1.5  11 years  overbeek  Update parsing of NAME field to reflect change in source file. -- /gdp
make_ma_html.pl  1.2  7 years  overbeek  minor fixes
make_maps_from_sub.py  1.5  12 years  olson  Add license words.
make_match_table.pl  1.2  12 years  olson  Add license words.
make_md5_figfams_file.pl  1.1  10 years  arodri7  script makes the md5 to figfams file
make_model_spreadsheets.pl  1.2  10 years  dejongh  switch to scenario_directory
make_ncbi_files.pl  1.4  11 years  wilke  changed check for existing directories
make_neigh_joining_tree.pl  1.8  11 years  overbeek  debugged version of bring_tree_up_to_ali
make_occ_counts.pl  1.2  12 years  olson  Add license words.
make_overlap_report.pl  1.22  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
make_parallel_proml_run.pl  1.2  11 years  overbeek  add rates to phylogeny stuff
make_partition_reps.pl  1.1  9 years  overbeek  try
make_partition_repsP.pl  1.4  9 years  arodri7  commit change
make_partition_repsW.pl  1.1  9 years  overbeek  try
make_partition_reps_worker.pl  1.3  9 years  arodri7  commit change
make_pdb_ontology.pl  1.3  10 years  mkubal  provides usage when no argument given
make_peg_map_from_tbl.pl  1.3  9 years  olson  fix bug that made empty output
make_peg_maps.pl  1.3  12 years  overbeek  minor fixes
make_peg_maps_from_fasta.pl  1.2  9 years  olson  need to compute sims both directions because connections_between now uses bbhs.
make_pfam_ontology.pl  1.4  10 years  mkubal  provides usage when no argument given
make_phob_from_ids.pl  1.3  12 years  olson  Add license words.
make_phob_from_seqs.pl  1.7  12 years  olson  Add license words.
make_pir_ontology.pl  1.3  10 years  mkubal  provides usage when no argument given
make_predictor_input.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
make_predictor_input_from_gto.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
make_probes_to_genes.pl  1.8  7 years  dejongh  check for same contig when matching probe to peg
make_proml_tree.pl  1.6  11 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
make_proml_tree_0.pl  1.1  11 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
make_proposed_assignments_for_consistency.pl  1.4  12 years  overbeek  fixes to wseekly statistics
make_prosite_ontology.pl  1.3  10 years  mkubal  provides usage when no argument given
make_protein_sets.pl  1.4  12 years  olson  Add license words.
make_protein_weights_and_rates.pl  1.2  11 years  golsen  Moving some tree building tools into packages.
make_rates.pl  1.2  12 years  olson  Add license words.
make_reduce_sims_index.pl  1.1  11 years  olson  new script
make_release.pl  1.5  3 years  olson  Add ProblemSets.current symlink management.
make_scored_instances.pl  1.5  5 years  overbeek  compute correspondences for a pan genome
make_sim_part_data.pl  1.1  9 years  overbeek  add command to build similarity partitions
make_sim_sets.pl  1.3  12 years  olson  Add license words.
make_sim_tab.pl  1.8  11 years  olson  compute_pchs_from_sims.pl
make_sims_and_fc_data.pl  1.1  9 years  overbeek  add wrapper to building partition-based similarity and fc data
make_sp_desc_with_org.pl  1.2  12 years  olson  Add license words.
make_sp_func_syn_dicts.pl  1.2  12 years  olson  Add license words.
make_sp_org_domain_table.pl  1.2  12 years  olson  Add license words.
make_sp_org_table.pl  1.2  12 years  olson  Add license words.
make_sp_uni_files.pl  1.4  11 years  wilke  changed check for input and output directory the directories may exists, so don'...
make_spreadsheet_and_notes.pl  1.3  12 years  olson  Add license words.
make_sprout_bbhs.pl  1.2  12 years  olson  Add license words.
make_sprout_upstream.pl  1.2  12 years  olson  Add license words.
make_sr_inconsistent_fams.pl  1.1  5 years  overbeek  build input for Bob to display
make_subsys_based_families.pl  1.14  10 years  overbeek  do not use genomes with variants beginning with an asterisk in forming FIGfams b...
make_subsys_based_families2.pl  1.1  9 years  arodri7  commit changes
make_subsystems_from_clusters.pl  1.5  12 years  olson  Add license words.
make_supporting_predicates.pl  1.3  6 years  overbeek  handle minor issue with compound predicate
make_tf_equivalog_file.pl  1.1  10 years  bartels  *** empty log message ***
make_timestamps.pl  1.4  11 years  overbeek  add initial version of FIGO.pm - OO services
make_transferable_chunks.pl  1.4  12 years  olson  Add license words.
make_transferable_tarfiles.pl  1.3  12 years  olson  Add license words.
make_trimmed_alignment_from_ids.pl  1.13  10 years  overbeek  return empty list of failure to open FIFfam
make_uniprot_corr.pl  1.2  10 years  overbeek  build uniprot correspondence
map-nr-ids-to-ncbi-std.pl  1.1  10 years  olson  Script to map IDs in a SEED NR into forms acceptable to the indexed NCBI fasta p...
map_pegs.pl  1.3  12 years  parrello  Fixed obsolete form of boundaries_of.
map_sims.pl  1.5  12 years  olson  Add license words.
map_sims_for_bigfc.pl  1.2  12 years  olson  Add license words.
map_to_scaffold.pl  1.4  10 years  olson  Actually write out the changed entries.
mark_genome_as_phage.pl  1.1  7 years  redwards  two phage specific scripts
mark_nr.pl  1.2  12 years  olson  Add license words.
mark_picked_genes.pl  1.2  9 years  overbeek  fix order of arguments
match_dna_to_aligned_prots.pl  1.4  12 years  olson  Add license words.
match_to_axes.pl  1.7  3 years  golsen  Fixed spelling errors in the documentation.
match_to_genome_axes.pl  1.2  6 years  golsen  Updated to use GenomeCodonUsages.pm
match_to_genome_frequencies.pl  1.3  6 years  golsen  Updated to use GenomeCodonUsages.pm
md5.c  1.3  12 years  olson  Doh, put proper comments in for C code.
merge_annotations.pl  1.3  12 years  olson  Add license words.
merge_assignments.pl  1.1  9 years  bartels  *** empty log message ***
merge_families.pl  1.3  11 years  overbeek  add strip comments argument on function_of
merge_gene_sets.pl  1.1  8 years  overbeek  code from Hope
merge_missing_gene_output.pl  1.3  8 years  olson  bugfix
merge_missing_sims.pl  1.1  5 years  redwards   a set of scripts for adding phage genomes to the seed
merge_peg_synonyms.pl  1.1  5 years  redwards   a set of scripts for adding phage genomes to the seed
merge_translation_rules.pl  1.7  12 years  olson  Add license words.
meta.pl  1.12  9 years  jared  added update_path
metagenome2genbank.pl  1.4  10 years  mkubal  includes data from meta.xml
mg_user_id_to_unique.pl  1.2  10 years  mkubal  full loop
modal_codon_usage.pl  1.2  6 years  golsen  Add full fasta description line to counts file.
modelCompare.pl  1.1  5 years  disz  Janaka reaction code
modify_tree.pl  1.1  8 years  golsen  A general purpose tree modification utility.
myjoin.pl  1.1  12 years  overbeek  fix building FigFamData
native_codon_usage.pl  1.1  6 years  golsen  Support for codon usage analyses.
new_versions_of_features.pl  1.1  12 years  overbeek  add new_versions_of_features
nmpdr2gff.pl  1.1  12 years  overbeek  RAE: Changes to gff3 files for NMPDR and adding nmpdr2gff for creating the files...
order_corrections_for_start_predictions.pl  1.5  10 years  gdpusch  Added FIGV support. -- /gdp
order_figfams.pl  1.1  12 years  overbeek  order_figfams
order_seqs_on_length.pl  1.1  11 years  overbeek  add utilities for computing alignments
order_sets.pl  1.3  12 years  olson  Add license words.
overlap_resolution_test.pl  1.2  4 years  golsen  Add a bunch of options to help in diagnosis, including feature list output and f...
p2p_daemon.pl  1.2  12 years  olson  Add license words.
p2p_sync_cron.pl  1.3  12 years  olson  Add license words.
p2p_sync_from_remote.pl  1.4  12 years  olson  Add license words.
p3-abstract-clusters.pl  1.2  7 months  parrello  Changes copied from SEEDtk project.
p3-aggregate-sss.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-aggregates-to-html.pl  1.6  7 months  parrello  Changes copied from SEEDtk project.
p3-all-drugs.pl  1.7  3 weeks  parrello  Changes copied from SEEDtk project.
p3-all-genomes.pl  1.8  3 weeks  parrello  Changes copied from SEEDtk project.
p3-blast.pl  1.4  2 months  parrello  Changes copied from SEEDtk project.
p3-build-kmer-db.pl  1.1  15 months  parrello  Changes from SEEDtk.
p3-closest-seqs.pl  1.2  14 months  parrello  Changes copied from SEEDtk project.
p3-co-occur.pl  1.2  3 weeks  parrello  Changes copied from SEEDtk project.
p3-collate.pl  1.1  2 months  parrello  Changes copied from SEEDtk project.
p3-count-families.pl  1.1  2 months  parrello  Changes copied from SEEDtk project.
p3-count.pl  1.2  7 months  parrello  Changes copied from SEEDtk project.
p3-drug-amr-data.pl  1.1  16 months  parrello  Changes copied from SEEDtk project.
p3-echo.pl  1.4  2 months  parrello  Changes copied from SEEDtk project.
p3-extract-gto.pl  1.6  7 months  parrello  Changes copied from SEEDtk project.
p3-extract.pl  1.6  2 months  parrello  Changes copied from SEEDtk project.
p3-feature-gap.pl  1.4  7 months  parrello  Changes copied from SEEDtk project.
p3-feature-upstream.pl  1.5  7 months  parrello  Changes copied from SEEDtk project.
p3-file-filter.pl  1.5  2 months  parrello  Changes copied from SEEDtk project.
p3-find-couples.pl  1.6  2 weeks  parrello  Changes copied from SEEDtk project.
p3-find-features.pl  1.4  3 weeks  parrello  Changes copied from SEEDtk project.
p3-find-in-clusters.pl  1.1  15 months  parrello  Changes from SEEDtk.
p3-format-results.pl  1.2  14 months  parrello  Changes copied from SEEDtk project.
p3-function-to-role.pl  1.3  15 months  parrello  Changes from SEEDtk
p3-generate-close-roles.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-generate-clusters.pl  1.4  15 months  parrello  Changes copied from SEEDtk project.
p3-genome-amr-data.pl  1.2  16 months  parrello  Changes copied from SEEDtk project.
p3-genome-fasta.pl  1.5  10 months  parrello  Changes copied from SEEDtk project.
p3-genus-species.pl  1.1  14 months  parrello  Changes copied from SEEDtk project.
p3-get-contig-data.pl  1.2  16 months  parrello  Changes copied from SEEDtk project.
p3-get-drug-genomes.pl  1.7  3 weeks  parrello  Changes copied from SEEDtk project.
p3-get-family-data.pl  1.6  3 weeks  parrello  Changes copied from SEEDtk project.
p3-get-family-features.pl  1.7  3 weeks  parrello  Changes copied from SEEDtk project.
p3-get-feature-data.pl  1.10  3 weeks  parrello  Changes copied from SEEDtk project.
p3-get-feature-group.pl  1.6  2 months  parrello  Changes copied from SEEDtk project.
p3-get-feature-sequence.pl  1.6  7 months  parrello  Changes copied from SEEDtk project.
p3-get-features-by-sequence.pl  1.2  10 months  parrello  Changes copied from SEEDtk project.
p3-get-genome-contigs.pl  1.5  3 weeks  parrello  Changes copied from SEEDtk project.
p3-get-genome-data.pl  1.10  3 weeks  parrello  Changes copied from SEEDtk project.
p3-get-genome-drugs.pl  1.8  3 weeks  parrello  Changes copied from SEEDtk project.
p3-get-genome-expression.pl  1.3  3 weeks  parrello  Changes copied from SEEDtk project.
p3-get-genome-features.pl  1.10  3 weeks  parrello  Changes copied from SEEDtk project.
p3-get-genome-group.pl  1.4  2 months  parrello  Changes copied from SEEDtk project.
p3-gto-dna.pl  1.1  14 months  parrello  Changes copied from SEEDtk project.
p3-gto-fasta.pl  1.1  15 months  parrello  Changes copied from SEEDtk project.
p3-gto-scan.pl  1.3  14 months  parrello  Changes copied from SEEDtk project.
p3-gto.pl  1.2  15 months  parrello  Changes from SEEDtk
p3-head.pl  1.1  15 months  parrello  Changes copied from SEEDtk project.
p3-identical-dna.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-identical-proteins.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-identify-clusters.pl  1.2  15 months  parrello  Changes copied from SEEDtk project.
p3-inAandB.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-inAnotB.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-inAorB.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-join.pl  1.2  3 weeks  parrello  Changes copied from SEEDtk project.
p3-kmer-compare.pl  1.2  7 months  parrello  Changes copied from SEEDtk project.
p3-list-feature-groups.pl  1.2  16 months  parrello  Changes copied from SEEDtk project.
p3-list-genome-groups.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-login.pl  1.6  16 months  parrello  Changes copied from SEEDtk project.
p3-mass-cluster-run.pl  1.2  14 months  parrello  Changes copied from SEEDtk project.
p3-match.pl  1.6  15 months  parrello  Changes copied from SEEDtk project.
p3-merge.pl  1.1  12 months  parrello  Changes copied from SEEDtk project.
p3-pick.pl  1.2  2 months  parrello  Changes copied from SEEDtk project.
p3-project-subsystems.pl  1.2  7 months  parrello  Changes copied from SEEDtk project.
p3-put-feature-group.pl  1.5  2 months  parrello  Changes copied from SEEDtk project.
p3-put-genome-group.pl  1.5  2 months  parrello  Changes copied from SEEDtk project.
p3-rast.pl  1.4  2 months  parrello  Changes copied from SEEDtk project.
p3-related-by-clusters.pl  1.8  14 months  parrello  Changes copied from SEEDtk project.
p3-rep-prots.pl  1.4  3 weeks  parrello  Changes copied from SEEDtk project.
p3-role-matrix.pl  1.2  2 months  parrello  Changes copied from SEEDtk project.
p3-sequence-profile.pl  1.3  11 months  parrello  Updates from SEEDtk
p3-set-to-relation.pl  1.3  15 months  parrello  Changes copied from SEEDtk project.
p3-signature-clusters.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-signature-families.pl  1.6  7 months  parrello  Changes copied from SEEDtk project.
p3-signature-peginfo.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-similar-proteins-by-blast.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-similar-proteins-by-family.pl  1.4  7 months  parrello  Changes copied from SEEDtk project.
p3-sort.pl  1.7  2 months  parrello  Changes copied from SEEDtk project.
p3-stats.pl  1.4  7 months  parrello  Changes copied from SEEDtk project.
p3-tbl-to-fasta.pl  1.2  7 months  parrello  Changes copied from SEEDtk project.
p3-tbl-to-html.pl  1.1  11 months  parrello  Changes copied from SEEDtk project.
p3-tests.pl  1.5  3 weeks  parrello  Changes copied from SEEDtk project.
p3_all_features.pl  1.1  3 years  olson  initial set of PATRIC data accessors. The p3* scripts have the same interface as...
p3_all_genomes.pl  1.1  3 years  olson  initial set of PATRIC data accessors. The p3* scripts have the same interface as...
p3_contigs_in_genome.pl  1.1  3 years  olson  initial set of PATRIC data accessors. The p3* scripts have the same interface as...
p3x-check-mcl-compute-times.pl  1.1  2 years  olson  P3 utility scripts.
p3x-compare-patric-calls-2.pl  1.1  2 years  olson  P3 utility scripts.
p3x-compare-patric-calls.pl  1.1  2 years  olson  P3 utility scripts.
p3x-compute-patric-update-delta.pl  1.1  13 months  olson  Add metadata to the query_cb callback. Also use the return value of query_cb to ...
p3x-compute-patric-update.pl  1.2  13 months  olson  Add metadata to the query_cb callback. Also use the return value of query_cb to ...
p3x-create-release-dir.pl  1.2  13 months  olson  Add metadata to the query_cb callback. Also use the return value of query_cb to ...
p3x-create-split-nr-for-fams.pl  1.1  2 years  olson  P3 utility scripts.
p3x-eval-bin-site.pl  1.2  3 weeks  parrello  Changes copied from SEEDtk project.
p3x-eval-bins.pl  1.2  3 weeks  parrello  Changes copied from SEEDtk project.
p3x-eval-genome.pl  1.1  2 months  parrello  Changes copied from SEEDtk project.
p3x-eval-genomes.pl  1.2  3 weeks  parrello  Changes copied from SEEDtk project.
p3x-eval-gto.pl  1.1  3 weeks  parrello  Changes copied from SEEDtk project.
p3x-eval-sort.pl  1.1  2 months  parrello  Changes copied from SEEDtk project.
p3x-propagate-family-names.pl  1.1  2 years  olson  P3 utility scripts.
p3x-recall-patric-proteins.pl  1.1  2 years  olson  P3 utility scripts.
p3x-recall-proteins.pl  1.1  2 years  olson  P3 utility scripts.
p3x-reduce-families-for-kser.pl  1.1  2 years  olson  P3 utility scripts.
p3x-setup-alignment-sync-dir.pl  1.1  4 months  olson  For P3 fam build, set up sync.dir
p3x-split-families.pl  1.1  2 years  olson  P3 utility scripts.
p3x-test-evaluator.pl  1.1  3 weeks  parrello  Changes copied from SEEDtk project.
p3x-update-propagated-family-names.pl  1.1  2 years  olson  P3 utility scripts.
p3x-write-family-defs.pl  1.1  17 months  olson  Extract local and global family definition files from full family data.
p3x-write-subsystem-qa.pl  1.1  14 months  olson  New module for patric subsystem QA
p3x_kser_parallel_load.pl  1.1  3 years  olson  Script to run a parallel load of kser with given nr data.
package_annotations.pl  1.9  12 years  olson  Add license words.
package_assignments.pl  1.8  12 years  olson  Add license words.
package_cleaned_bins.pl  1.3  2 months  parrello  Changes copied from SEEDtk project.
package_code.pl  1.2  12 years  olson  Add license words.
package_fix.pl  1.1  11 months  parrello  Changes copied from SEEDtk project.
package_lightweight_code.pl  1.2  12 years  olson  Add license words.
package_raw_data_for_transplant.pl  1.2  12 years  olson  Add license words.
package_sims.pl  1.2  12 years  olson  Add license words.
package_subsystems.pl  1.6  7 months  parrello  Changes copied from SEEDtk project.
package_translation_rules.pl  1.2  12 years  olson  Add license words.
paint_reactions_on_tree_pipeline.pl  1.2  5 years  overbeek  trying to commit a working copy
paint_tree.pl  1.3  12 years  olson  Add license words.
parse_genbank.pl  1.34  3 years  gdpusch  Fixed parsing failure in case when TAXONOMY string consists of a single field wi...
parse_mart.py  1.6  12 years  olson  Add license words.
parse_uniparc.pl  1.1  11 years  mkubal  v1
partition_prots.pl  1.5  5 years  overbeek  compute correspondences for a pan genome
patric_call_proteins.pl  1.4  2 years  olson  reduce fig obj creation
peg2pubmed.pl  1.1  12 years  hwang  Added two scripts that will generate pubmed files
peg_to_name.pl  1.4  12 years  olson  Add license words.
peg_to_pdb.py  1.2  12 years  olson  Add license words.
peg_to_subsystems.pl  1.3  12 years  olson  Add license words.
pegs.pl  1.3  12 years  olson  Add license words.
pegs_in_conflict.pl  1.3  12 years  olson  Add license words.
pegs_in_subsystem.pl  1.6  9 years  overbeek  check for aux roles
pegs_in_subsystems.pl  1.8  9 years  overbeek  fix documentation
pegs_on_contigs.pl  1.2  22 months  parrello  Changes copied from SEEDtk project.
pg_add_genomes.pl  1.1  5 years  overbeek  add RAST genomeIDs to genome table
pg_add_role_peg.pl  1.4  5 years  overbeek  bad stuff
pg_adjacency_of_core.pl  1.2  5 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_build_fasta_for_phylogeny.pl  1.5  5 years  overbeek  updates induced by Bob
pg_build_newick_tree.pl  1.2  4 years  overbeek  use muscle for alignments
pg_build_protein_families.pl  1.4  5 years  overbeek  fixes to pan-genera pipeline
pg_check_gapfills.pl  1.1  5 years  overbeek  add gapfilling
pg_compute_corr.pl  1.3  5 years  overbeek  handle extraction of genome id better
pg_compute_md5s.pl  1.1  5 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_compute_subsystem_membership.pl  1.1  5 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_compute_traits.pl  1.3  5 years  overbeek  fix to pass2
pg_core_families.pl  1.8  5 years  overbeek  minor fix
pg_estimate_alien_pegs.pl  1.3  5 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_events.pl  1.2  5 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_extract_reaction_sets.pl  1.4  5 years  overbeek  fix eol
pg_filter_alien.pl  1.1  5 years  overbeek  reorder alien computation
pg_form_mobile_element_families.pl  1.3  5 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_function_of.pl  1.2  5 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_generate_possible_assignments.pl  1.1  5 years  overbeek  pg pipeline
pg_get_codon_usage_stats.pl  1.1  5 years  overbeek  add codon usage
pg_get_consistency_before_after.pl  1.2  5 years  overbeek  handle no assignments
pg_get_gapfill_reactions.pl  1.1  5 years  overbeek  add gapfilling
pg_get_models.pl  1.1  5 years  overbeek  add gapfilling
pg_get_pegs_in_repeats.pl  1.3  5 years  overbeek  set min overlap to 50
pg_get_reaction_keys.pl  1.1  5 years  overbeek  add gapfilling
pg_get_reaction_role.pl  1.1  5 years  overbeek  add gapfilling
pg_get_reactions.pl  1.1  5 years  overbeek  add gapfilling
pg_get_stats.pl  1.3  5 years  overbeek  fixes due to using nonRAST genomes
pg_inconsistent_families.pl  1.4  5 years  overbeek  strip comments
pg_intersection.pl  1.1  5 years  overbeek  add Jose stuff
pg_janaka_get_role_reactions_pegs.pl  1.4  5 years  overbeek  get rid of comments on functions
pg_make_initial_models.pl  1.12  5 years  overbeek  watch out for failing models
pg_make_md5_families.pl  1.5  5 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_make_reaction_properties.pl  1.1  5 years  overbeek  make reaction properties to paint tree
pg_make_reaction_tables.pl  1.1  5 years  overbeek  extract reaction table
pg_pipeline.pl  1.51  5 years  overbeek  readdble.tree is in Analysis
pg_process_pubs.pl  1.1  5 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_roles_in_some_but_not_X.pl  1.9  5 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_run_gapfills.pl  1.1  5 years  overbeek  add gapfilling
pg_submit_to_RAST.pl  1.3  5 years  overbeek  taxon id - not debugged
pg_tabulate_reactions.pl  1.2  5 years  overbeek  compute core reactions
pick_feature_set.pl  1.1  9 years  overbeek  choose genes from candidates
place_properties_on_tree.pl  1.6  3 years  overbeek  BAD BUG
place_proteins_into_pattyfams.pl  1.8  23 months  olson  Workaround for broken kser.
plate_sheet_parser.pl  1.1  3 weeks  parrello  Changes copied from SEEDtk project.
pop_vec.pl  1.2  5 years  overbeek  compute correspondences for a pan genome
possible_frameshifts.pl  1.1  11 years  overbeek  update possible_frameshifts
possible_projections.pl  1.1  6 years  overbeek  for veronika projections
possibly_truncated.pl  1.2  12 years  olson  Add license words.
postprocess_computed_sims.pl  1.2  12 years  olson  Add license words.
potentially_cotranscribed.pl  1.2  12 years  olson  Add license words.
potentially_missed_assignments.pl  1.1  12 years  overbeek  add potentially_missed_assignments
pp.pl  1.3  12 years  olson  Add license words.
predict_scenarios.pl  1.2  11 years  formsma  Added code to automatically run 'run_scenarios All' if it hasn't been run. These...
predict_starts.pl  1.8  10 years  gdpusch  Added FIGV support. -- /gdp
predicted_vs_actual.pl  1.1  9 years  overbeek  basic metagenomic tools
prep_viz.pl  1.2  12 years  olson  Add license words.
prepare_metagenome_files_for_download.pl  1.4  10 years  mkubal  full loop
prepare_metagenome_files_for_ftp.pl  1.3  10 years  mkubal  checks for PUBLIC file
process_evaluation.pl  1.1  22 months  parrello  Changes copied from SEEDtk project.
process_genomes.pl  1.1  7 years  disz  Format new genomes for the Daily SEED
process_new_sims.pl  1.6  11 years  olson  Rollup of various rast-related changes.
process_one_exp_dir.pl  1.4  7 years  olson  fix typo
process_otus.pl  1.8  5 years  overbeek  do not use ref in sparse
process_sim_deletions_and_replacements.pl  1.3  12 years  olson  Add license words.
project.pl  1.2  12 years  olson  Add license words.
project_codon_usage_onto_axis.c  1.1  6 years  golsen  Support for codon usage analyses.
promote_orfs_to_pegs.pl  1.15  7 years  gdpusch  Code restructured, and modified to fail gracefully if there are no closest genom...
propagate_subsys_changes_to_figfams.pl  1.12  9 years  arodri7  commit changes
pubbed_fids.pl  1.1  9 years  parrello  New script to find features with publications attached.
publish_subsystems.pl  1.1  6 years  olson  script to programmagically publish a subsystem
pubmed_gene2peg.pl  1.2  12 years  redwards  making sure gene id is right
pubseed_data_export.pl  1.1  5 years  olson  Data exporter for pubseed.
pull_fasta_entries.pl  1.8  9 years  olson  do not attempt to remap incoming ids
pull_orfs.pl  1.8  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
pull_sp_entries.pl  1.2  12 years  olson  Add license words.
purge_fasta.pl  1.1  12 years  overbeek  Removes duplicate entries from fasta file. -- /gdp
purge_tbl.pl  1.1  12 years  overbeek  Removes duplicate entries from tbl file. -- /gdp
put_directory_in_one_file.pl  1.2  12 years  olson  Add license words.
put_func_on_families_2c.pl  1.1  5 years  overbeek  get funcs
questionable_calls.pl  1.2  12 years  olson  Add license words.
rapid_propagation.pl  1.75  9 years  olson  use $num_neighbors internally instead of hardwired constant
rapid_propagation2.pl  1.5  8 years  gdpusch  Minor cosmetic changes.
rapid_propagation3.pl  1.10  8 years  olson  Support family determiantion.
rapid_propagation4.pl  1.11  22 months  gdpusch  Finally fixed (I hope!) the "Undefined Domain" bug.
rapid_propagation5.pl  1.2  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
rapid_propagation_plasmid.pl  1.22  8 years  disz  FigFam 6 digit problem
rapid_subsystem_inference.pl  1.22  3 years  overbeek  fix duplicate code
rapid_subsystem_inference_batch.pl  1.4  7 years  olson  Fix null-key bug
rast_annotate_proteins_similarity.pl  1.4  5 weeks  olson   Don't require KB IDserver
rast_build_nr_from_close_genomes.pl  1.1  5 weeks  gdpusch  Initial checkin. Script to build and formatdb a local NR in a RAST directory fro...
rast_call_CDSs_using_prodigal.pl  1.7  5 weeks  olson  Modifications for compiling without KB IDServer module. Add assembly gap caller....
rast_call_RNAs.pl  1.3  3 years  olson  Propagate production fixes.
rast_call_assembly_gaps.pl  1.1  5 weeks  olson  Modifications for compiling without KB IDServer module. Add assembly gap caller....
rast_call_crisprs.pl  1.6  5 weeks  olson  Don't require KB IDServer
rast_call_prophage_using_phispy.pl  1.6  5 weeks  olson  Modifications for compiling without KB IDServer module. Add assembly gap caller....
rast_call_rRNAs.pl  1.9  5 weeks  olson  Don't require KB idserver
rast_call_special_proteins.pl  1.13  5 weeks  olson  Modifications for compiling without KB IDServer module. Add assembly gap caller....
rast_call_tRNAs.pl  1.6  5 weeks  olson  Modifications for compiling without KB IDServer module. Add assembly gap caller....
rast_compute_specialty_genes.pl  1.6  13 months  olson  Update to use blat and new thresholds.
rast_export_genome.pl  1.25  4 months  olson  Fix tax ID in export.
rast_load_specialty_genes.pl  1.2  4 years  olson  Specialty protein & PATRIC caller code.
rast_prepare_NR_directory.pl  1.1  4 years  olson  annotate via similarity scripts
rationalize_blast.pl  1.5  4 years  golsen  Fixed one typo in an error message.
read_write_excel.pl  1.1  12 years  overbeek  RAE: Initial release of a simple script to read and write excel files to allow e...
readable_fasta.pl  1.1  6 years  overbeek  initial versions
rebuild_converged_Data.pl  1.7  2 years  olson  Commit updates to kmer build code.
rebuild_global_chromosomal_clusters.pl  1.2  11 years  overbeek  version of rebuild_global_chromosomal_clusters that works
recall_pegs.pl  1.2  6 years  overbeek  add blocked robot
recent_annotations_by_genome.pl  1.1  6 years  disz  create data for the Daily SEED
recompute_comparison.pl  1.1  10 years  bartels  *** empty log message ***
reduce_sims.pl  1.12  9 years  olson  fix nasty little bug that drops sims
reformat_circular_contigs.pl  1.1  9 years  arodri7  added reformat_circular_contigs for rapid_propagation_plasmids
reformat_contigs.pl  1.26  20 months  gdpusch  Fixed missing argument-type for --logfile argument
reformat_dsim_dbs.pl  1.2  12 years  olson  Add license words.
reformat_fasta.pl  1.2  12 years  olson  Add license words.
reformat_sims.pl  1.8  11 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
reformat_timelogic_sims.pl  1.2  11 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
register_features_batch.pl  1.2  12 years  olson  Add license words.
register_features_with_clearinghouse.pl  1.2  12 years  olson  Add license words.
register_genome_with_clearinghouse.pl  1.1  11 years  olson  Missing scripts.
reindex_sim_btrees.pl  1.1  6 years  olson  new script to update btree indexes of sims files in a genome dir
rel2tabs.pl  1.3  3 years  parrello  Changes copied from SEEDtk project.
relabel_nodes.pl  1.2  12 years  olson  Add license words.
relevant_PCHs.pl  1.3  12 years  olson  Add license words.
relevant_pchsG.pl  1.4  12 years  olson  Add license words.
remove_clustered_pchs.pl  1.10  11 years  overbeek  fix rfemove_clustered_PCHs to count correctly
remove_clustered_pchs2.pl  1.1  11 years  olson  Missing scripts.
remove_clustered_pchs3.pl  1.1  11 years  olson  Missing scripts.
remove_embedded_pegs.pl  1.19  8 years  gdpusch  Modified to use Kmers.
remove_multiple_occurring_probes.pl  1.2  7 years  olson  exp fixes
remove_rna_overlaps.pl  1.11  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
remove_sims_not_in_nr.pl  1.1  11 years  olson  Missing scripts.
renumber_features.pl  1.14  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
renumber_seed_dir.pl  1.8  20 months  gdpusch  Somewhat dangerous fix to the sims files
rep_genomes.pl  1.1  11 years  overbeek  fixes to representative tree generation and added rep_genomes
rep_sets.pl  1.1  9 years  disz  Old code finally checked in to create representative sets
report_changes.pl  1.2  12 years  olson  Add license words.
representative_tree.pl  1.2  12 years  olson  Add license words.
reps_and_close.pl  1.2  11 years  overbeek  add make_trimmed_alignment_from_ids
reps_for_wc.pl  1.2  3 years  jdavis  updated usage statement
restore_annotations.pl  1.2  12 years  olson  Add license words.
restore_assignments.pl  1.2  12 years  olson  Add license words.
restore_translation_rules.pl  1.2  12 years  olson  Add license words.
restrict_by_similarity.pl  1.4  12 years  olson  Add license words.
restrict_to_genomes.pl  1.3  12 years  olson  Add license words.
rewrite_peg_syns.pl  1.1  5 years  redwards   a set of scripts for adding phage genomes to the seed
roles_in_subsystem.pl  1.2  12 years  olson  Add license words.
root_at.pl  1.2  12 years  olson  Add license words.
root_at_midpoint.pl  1.1  4 years  overbeek  root a tree at the midpoint
rs.pl  1.2  4 years  overbeek  compute mean/stddev of positive hits
rs_create_ref_profile.pl  1.1  5 years  overbeek  the rna_seq pipeline
rs_get_intergenic_counts.pl  1.1  5 years  overbeek  the rna_seq pipeline
rs_get_peg_counts.pl  1.1  5 years  overbeek  the rna_seq pipeline
rs_get_rnas.pl  1.1  5 years  overbeek  the rna_seq pipeline
rs_pipeline.pl  1.1  5 years  overbeek  the rna_seq pipeline
run1_convergence_step.pl  1.7  2 years  olson  Commit updates to kmer build code.
run_HMM_search_on_timelogic.pl  1.1  11 years  mkubal  version 1.0
run_all_fam_rel.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
run_all_inference.pl  1.2  7 years  olson  Run on all genomes; update anything either missing a subsystems file or that hav...
run_anno_to_pubseed_flow.sh  1.6  5 years  olson  fix missing \
run_checkm.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
run_coreseed_to_pubseed_flow.sh  1.1  5 years  olson  Support for annotation flow from CoreSEED to PubSEED.
run_fc.pl  1.2  12 years  olson  Add license words.
run_find_subsys_against_all_genomes.pl  1.2  11 years  overbeek  updates to computation of VCs
run_flux_optimization.pl  1.4  10 years  dejongh  switch to scenario_directory
run_gene_calling_scripts.pl  1.3  9 years  overbeek  fix first arg on call to mark_picked_genes
run_glimmer2.pl  1.7  11 years  gdpusch  Added support for multiple genetic codes. -- /gdp
run_glimmer3.pl  1.14  8 years  parrello  Added "-verbose" option so tracing can be turned on from the servers.
run_model_generation.pl  1.17  10 years  dejongh  switch to scenario_directory
run_model_generation_all.pl  1.1  11 years  formsma  This script will generate models for all complete genomes in the seed. - Kevin
run_model_generation_v3.pl  1.3  10 years  dejongh  switch to scenario_directory
run_muscle.pl  1.3  7 years  golsen  Update libraries used.
run_peg_job_worker.pl  1.4  12 years  olson  Add license words.
run_rabbit_daemon.pl  1.5  6 years  olson  Add memcached support
run_rabbit_daemon_set.pl  1.3  7 years  olson  remove debug
run_remote_PHOBIOUS.pl  1.1  11 years  mkubal  runs Phobius computation for given geneome
run_remote_Phobius_for_fasta.pl  1.1  10 years  mkubal  fasta file as input
run_remote_Phobius_for_genome.pl  1.1  11 years  mkubal  for single genome
run_remote_Phobius_for_genome_for_RAST.pl  1.1  11 years  mkubal  for use with RAST server
run_remote_Phobius_for_genomes.pl  1.1  11 years  mkubal  run for all complete prok genomes
run_ribo_ratio_against_pubseed.pl  1.1  5 years  overbeek  quality control using ribo proteins
run_scenarios.pl  1.5  10 years  dejongh  switch to scenario_directory
run_start_predictions_for_all_subsystems.pl  1.4  12 years  olson  Add license words.
run_start_predictions_for_spreadsheet.pl  1.6  12 years  olson  Add license words.
runclustalw.pl  1.4  11 years  overbeek  add computation of alignments to building FIGFAMS
salvage_annotations.pl  1.6  12 years  olson  bugfix.
salvage_master_annotations.pl  1.3  12 years  overbeek  fixes to salvage code
salvage_subsystem_rows.pl  1.6  12 years  overbeek  fixes to salvage code
same_figfam.pl  1.2  11 years  overbeek  handle bad input in same_figfam
same_subsys.pl  1.1  12 years  overbeek  fixes to extract_genomes
score_dfcs.pl  1.3  12 years  overbeek  RAE: removing the header that should not be in the source
score_dfcs_mcauliffe.pl  1.5  12 years  overbeek  limit decimal positions in score
score_ifcs.pl  1.4  12 years  overbeek  RAE: More direct and indirect functional coupling scores
score_ifcs_mcauliffe.pl  1.2  12 years  overbeek  RAE: correcting indirect functional coupling score
seed2genbank.pl  1.6  6 years  redwards  adding SOURCE and taxonomy information
seed2gff.pl  1.36  10 years  redwards  getting rid of need for strain info
seed2pir.pl  1.3  12 years  overbeek  RAE: moving PIRSF to links
seed2ptt.pl  1.2  5 years  redwards  adding alternate genome selections
seed2tbl.pl  1.3  8 years  disz  FigFam 6 digit problem
seed2txt.pl  1.1  7 years  olson  create spreadsheet of SEED org
seed_job_scheduler.pl  1.4  4 years  olson  add pid file argument
seed_run_job.pl  1.4  12 years  olson  readonly fixes; seed-run-job update to run from input file
seed_run_task.pl  1.2  12 years  olson  readonly fixes; seed-run-job update to run from input file
select_genomes_for_sprout.pl  1.2  12 years  olson  Add license words.
sequence_dereplication.pl  1.1  9 years  arodri7  first version of sequence_dereplication. Script takes sequences which are subset...
sequence_length_histogram.pl  1.6  8 years  olson  Include in SAS
server_paper_example1.pl  1.12  8 years  parrello  Documentation fix for server paper.
server_paper_example2.pl  1.7  8 years  disz  Changed to use ANNO server
server_paper_example3.pl  1.5  8 years  disz  converted to new SAP server
server_paper_example4.pl  1.3  8 years  parrello  Fixed to use the correct servers.
server_paper_example5.pl  1.3  8 years  disz  Switched to ANNO server
server_paper_example6.pl  1.3  8 years  parrello  Fixed for server paper.
server_paper_example7.pl  1.4  8 years  chenry  Corrected a few bugs in the example script.
server_paper_figure2.pl  1.2  8 years  parrello  Removed genetic codes so program fits better on a page.
set-from-subtree.pl  1.1  17 months  parrello  Changes copied from SEEDtk project.
set_by_subtree.pl  1.1  17 months  parrello  Changes copied from SEEDtk project.
set_figfam_functions.pl  1.1  6 years  overbeek  to support assigning FigFam functions
set_not_private.pl  1.1  10 years  bartels  *** empty log message ***
set_to_relation.pl  1.2  12 years  olson  Add license words.
show_reconfig_cmd.pl  1.3  12 years  olson  Add license words.
show_structured_english.pl  1.1  10 years  disz  Ross's code to generate annotations for NCBI
sigs.pl  1.2  6 years  overbeek  slight change of parameters with better tests
similar_to.pl  1.4  12 years  olson  Add license words.
sims_after_adding_genome.pl  1.1  5 years  redwards   a set of scripts for adding phage genomes to the seed
sims_all.pl  1.6  9 years  overbeek  remove paralogs before computing conections
sims_between.pl  1.7  11 years  overbeek  updates on close connections
sketch_tree.pl  1.5  5 years  olson  Revive this script.
solid_rectangles_to_solid_families.pl  1.1  5 years  overbeek  format output
sort_and_split_bbhs.pl  1.5  11 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
sort_by_annotator.pl  1.2  7 years  disz  Fixed bad links
sort_by_function.pl  1.2  7 years  disz  Fixed find old function
sort_sets_of_pegs.pl  1.1  5 years  overbeek  sort a set of peg sets
sp2fasta.pl  1.2  12 years  olson  Add license words.
sparse_genome_sample.pl  1.1  5 years  golsen  A script to provide a set of diverse genomes (< 90% identical) that are similar ...
sphinx_index_genome.pl  1.14  2 years  olson  fix indexing bug with unanticipated feature types.
split_and_install_pchs.pl  1.2  12 years  olson  Add license words.
split_and_trim_sequences.pl  1.14  11 years  overbeek  fix problem when repeats occur
split_assignments_based_on_subsystems.pl  1.1  12 years  overbeek  next version of the STAG code
split_by_genome.pl  1.1  12 years  overbeek  split_by_genome can be used to split a score or BBH file
split_clean_unclean_families.pl  1.4  12 years  overbeek  fixes for splitting families into clean/unclean
split_fasta.pl  1.1  3 years  olson  Script to split a fasta file into chunks of a given size.
split_sequences_into_sets.pl  1.5  9 years  overbeek  handle asym connections
split_sims.pl  1.3  12 years  olson  Add license words.
splitup.pl  1.4  12 years  olson  Add license words.
sprout_search.pl  1.2  12 years  olson  Add license words.
sr_pipeline.pl  1.3  5 years  overbeek  mixed pipelines
start_data_for_set_of_pegs.pl  1.6  10 years  gdpusch  Added FIGV support. -- /gdp
start_dbserver.pl  1.3  3 years  golsen  Added the $dont_fork parameter to the start_server call, based upon the value of...
start_services.pl  1.12  12 years  olson  Add license words.
stop_services.pl  1.5  12 years  olson  Add license words.
submit_corr.pl  1.1  6 years  overbeek  create new saved correspondences
submit_corr_to_server.pl  1.2  6 years  overbeek  fefault value for map submission
submit_ff_test.pl  1.6  9 years  arodri7  commit changes
submit_genome_to_rpsblast_against_CDD_on_biocluster.pl  1.2  11 years  mkubal  test for dir exist
submit_genome_to_signalP.pl  1.2  11 years  mkubal  test for dir exist
submit_to_iprscan_on_biocluster.pl  1.1  11 years  mkubal  run iprscan on cluster
subsys2pubmed.pl  1.4  11 years  hwang  change script to add new attribute after each subsystem versus after all subsyst...
subsys_info.pl  1.1  10 years  overbeek  subsys_info is subsystem information for Verionika
subtree_of.pl  1.2  12 years  olson  Add license words.
summarize_classification_data.pl  1.1  5 years  overbeek  summarize classification output
summarize_genome_data.pl  1.1  5 years  overbeek  create summary_of_genome data
summarize_taxonomy_by_blast.pl  1.9  10 years  redwards  removing fatal error if 0 or 1 hits
svc_fasta_to_md5.pl  1.2  2 years  parrello  Changes copied from SEEDtk project.
svr.pl  1.2  8 years  olson  add . to include path
svr_ACH.t  1.1  8 years  olson  new tests
svr_CS.pl  1.9  10 months  olson  add p3 support
svr_CS_pipeline.pl  1.6  4 years  overbeek  compute adjacency data for What Changed?
svr_NCBI_sequence.pl  1.1  3 years  golsen  A script for retrieving sequence and related data from NCBI. Output can be tab d...
svr_NCBI_taxonomy.pl  1.2  7 years  golsen  Add more formats in which abbreviated lineages can be returned. Add long form of...
svr_RNA_genes.pl  1.6  3 years  golsen  Improve comments.
svr_SAP.t  1.4  8 years  olson  update tests
svr_ach_lookup.pl  1.10  8 years  parrello  More server script stuff. Thought I'd already installed these last week...
svr_add_lengths_to_blast.pl  1.1  7 years  overbeek   simple utility to add sequence lengths to m8 blast output
svr_add_reaction_descriptions.pl  1.1  5 years  overbeek  a tool to add reaction descriptions
svr_ali_to_html.pl  1.4  6 years  fangfang  fixed bug for the no color option by using Gary's new repad_alignment code
svr_aliases_of.pl  1.7  7 years  parrello  Fixed for better flow control.
svr_aliases_to_pegs.pl  1.1  8 years  parrello  New script for Ross
svr_align_seqs.pl  1.15  6 years  overbeek  allow option to preserve sequence order
svr_align_using_muscle.pl  1.2  8 years  gdpusch  Fixed incorrect function names.
svr_aligns_with_prot.pl  1.1  4 years  golsen  Provide a command line mechanism to get the alignments associated with one or mo...
svr_all_complexes.pl  1.1  6 years  parrello  New script to return all complexes.
svr_all_experiments.pl  1.1  7 years  parrello  Added to get experiments for each genome.
svr_all_features.pl  1.7  7 years  olson  Deobfuscate the command line logic. Submit requests in chunks so as to not be pa...
svr_all_figfams.pl  1.2  8 years  parrello  Documentation fixes.
svr_all_genomes.pl  1.3  7 years  overbeek  support restriction to proks
svr_all_models.pl  1.2  7 years  overbeek  keep only Seed models
svr_all_reactions.pl  1.1  7 years  parrello  New chemistry-based scripts.
svr_all_roles_used_in_models.pl  1.1  6 years  parrello  New command for roles found in models.
svr_all_subsystems.pl  1.9  8 years  parrello  Fixed POD errors. Added examples.
svr_assign_to_dna_using_figfams.pl  1.18  6 years  olson  add prot length and genus
svr_assign_using_figfams.pl  1.13  4 years  overbeek  describe output more accurately
svr_atomic_reg_coexp.pl  1.1  6 years  overbeek  initial version
svr_atomic_regulons.pl  1.1  7 years  parrello  Added to allow retrieval of pegs in atomic regulons.
svr_big_repeats.pl  1.3  4 years  olson  add error message to failure messages
svr_blast.pl  1.2  4 years  overbeek  compute mean/stddev of positive hits
svr_by_taxonomy.pl  1.3  8 years  overbeek  fix parameter passing
svr_call_pegs.pl  1.2  8 years  overbeek  fix POD stuff
svr_call_rnas.pl  1.2  7 years  overbeek  fix pod doc
svr_cdd_scan.pl  1.3  7 years  fangfang  retrieve non-specific hits for full mode
svr_close_genomes.pl  1.2  5 years  overbeek  compute correspondences for a pan genome
svr_closest_genes.pl  1.1  8 years  parrello  More server script stuff.
svr_cluster_locations.pl  1.1  4 years  overbeek  compute clusters
svr_cluster_pegs.pl  1.1  7 years  overbeek  two small utilities
svr_co_occurrence_evidence.pl  1.4  8 years  disz  FigFam 6 digit problem
svr_cohesion_groups.pl  1.4  7 years  fangfang  update
svr_column_of_subsystem.pl  1.1  8 years  olson  server script to pull a subsystem colum
svr_compare_feature_tables.pl  1.7  8 years  gdpusch  Fixed typo in variable-name
svr_complex_to_reaction.pl  1.1  6 years  parrello  New script to connect complexes to reactions.
svr_condense_repeats.pl  1.3  4 years  overbeek  throw out overlapping
svr_contigs_in_genome.pl  1.3  8 years  parrello  Added support for specifying input IDs on the command line.
svr_copy_to_RAST_dir.pl  1.3  8 years  olson  fix
svr_coregulated_by_correspondence.pl  1.7  5 years  overbeek  compute correspondences for a pan genome
svr_corr_by_exp.pl  1.5  7 years  parrello  Changed to batch the input instead of slurping it.
svr_corresponding_genes.pl  1.24  8 years  overbeek  fix command line arguments
svr_corresponding_genes2.pl  1.7  2 years  olson  Revert to 1.5.
svr_coupled_reactions.pl  1.1  7 years  parrello  New chemistry-based scripts.
svr_create_set.pl  1.1  7 years  disz  New persistent set svr scripts
svr_current_annotation.pl  1.4  5 years  fangfang  fix bug
svr_cut_domain.pl  1.1  8 years  overbeek  cut domains from sequences
svr_delete_RAST_job.pl  1.3  9 years  olson  Fix 666666 problem. Add support for using the test server.
svr_delete_from_set.pl  1.1  7 years  disz  New persistent set svr scripts
svr_delete_set.pl  1.1  7 years  disz  New persistent set svr scripts
svr_determine_sets_of_related_contigs.pl  1.4  8 years  parrello  Documentation fixes.
svr_discriminating_functions.pl  1.3  8 years  parrello  Discrimination functions support scripts.
svr_distinct_otus.pl  1.4  8 years  parrello  Added support for specifying input IDs on the command line.
svr_dlits.pl  1.1  7 years  parrello  New script to call dlits_for_ids
svr_dna_seq.pl  1.2  8 years  parrello  More server script stuff.
svr_drug_resistance_proteins.pl  1.3  4 years  fangfang  fix merge conflict
svr_enumerate_sets_by_owner.pl  1.1  7 years  disz  New persistent set svr scripts
svr_evidence.pl  1.1  8 years  disz  New svr script to get evidence code
svr_exp_genomes.pl  1.1  7 years  parrello  New script to list expression-data genomes.
svr_export_as_seed_dir.pl  1.3  7 years  olson  bugfix, get all subsystem records.
svr_expressed_genes_in_range.pl  1.1  7 years  parrello  Added for looking at genes that are never or always expressed.
svr_fasta.pl  1.14  7 years  overbeek  wrap the seq into 60-char lines
svr_fasta_to_md5.pl  1.1  7 years  parrello  New script for computing MD5s from FASTA protein sequences.
svr_fc_figfams.pl  1.3  8 years  overbeek  sort by score
svr_fids_for_md5.pl  1.1  7 years  parrello  New method to return FIG IDs for a protein given its MD5.
svr_fids_to_ids.pl  1.1  5 years  gdpusch  Initial checkin of script to fetch external ("alias") IDs for a FID.
svr_fids_to_locations.pl  1.1  4 years  overbeek  get locations of fids
svr_fids_to_regulons.pl  1.1  6 years  parrello  New script to find regulons for features.
svr_fig_id_corr.pl  1.4  8 years  overbeek  add -precise option
svr_figfam_fasta.pl  1.5  8 years  parrello  More server script stuff. Thought I'd already installed these last week...
svr_figfam_functions.pl  1.2  8 years  parrello  Added option to get all the FIGfams.
svr_figfams_to_ids.pl  1.6  8 years  parrello  Added "roles_to_subsys", sped up "figfams_to_ids", fixed pod for "mapped_genomes...
svr_file_to_spreadsheet.pl  1.3  7 years  olson  If -u url flag is added, add links to pegs.
svr_find_clusters_relevant_to_reaction.pl  1.6  5 years  overbeek  compute correspondences for a pan genome
svr_find_fused_genes.pl  1.3  7 years  fangfang  updated POD
svr_find_hypos_for_cluster.pl  1.1  7 years  overbeek  find hypotheticals associated with clusters
svr_find_protein.pl  1.2  7 years  parrello  Fixed the error reporting.
svr_find_regulatory_proteins.pl  1.1  8 years  overbeek  a simple tool to find potential regulatory proteins
svr_function_of.pl  1.15  4 years  parrello  CDMI and Sprout load fixes. Locations fixes.
svr_function_to_role.pl  1.1  6 years  parrello  New script for converting functions to roles.
svr_functionally_coupled.pl  1.2  7 years  overbeek  add cutoffs
svr_gap_filled_reactions_and_roles.pl  1.5  7 years  devoid  fixing some problems with authentication, error reporting
svr_genbank_to_seed.pl  1.4  20 months  gdpusch  Extract RNAs as well as PEGs.
svr_genbank_to_table.pl  1.2  8 years  gdpusch  Added various alias IDs to output.
svr_gene_data.pl  1.3  8 years  parrello  First round of script updates & additions for tutorial.
svr_generate_dna_samples.pl  1.1  5 years  overbeek  basic kmer validation tools
svr_genome_functions.pl  1.3  8 years  overbeek  sort by feature id
svr_genome_of.pl  1.1  6 years  overbeek  genome of feature
svr_genome_statistics.pl  1.2  8 years  parrello  Added genome name to the POD.
svr_get_ali_and_tree.pl  1.1  7 years  overbeek  get alignment and tree from seq(s)
svr_get_all.pl  1.2  5 years  olson  Make array-valued fields be returned as comma-joined.
svr_get_coupling_data.pl  1.2  7 years  overbeek  must have -d
svr_get_default_dataset.pl  1.1  7 years  olson  script to retrieve the name of the current default kmer datasets
svr_get_rep_genomes.pl  1.2  5 years  overbeek  minor fix of documentation
svr_get_set.pl  1.2  7 years  disz  New persistent set svr scripts
svr_identical_genomes.pl  1.2  6 years  overbeek  return seed, as well
svr_ids_to_figfams.pl  1.8  8 years  overbeek  fixes to documentation
svr_ids_to_subsystems.pl  1.6  8 years  disz  Added stderr output for non-matches
svr_img_analysis.pl  1.5  6 years  parrello  Converted to new interface.
svr_in_fasta.pl  1.1  5 years  overbeek  compute correspondences for a pan genome
svr_in_runs.pl  1.5  8 years  parrello  Fixed POD errors. Added examples.
svr_inconsistent_sets.pl  1.5  7 years  overbeek  minor fixes
svr_inherit_aliases.pl  1.5  7 years  gdpusch  Fixed mapping failure.
svr_inherit_annotations.pl  1.3  7 years  gdpusch  Saved ouput of ID mapping to file "inheritance.id_map," and added some bulletpro...
svr_insert_seqs_into_alignment.pl  1.2  8 years  fangfang  take advantage of gjoseqlib's flexible API to implicitly interact with STDIN/STD...
svr_intergenic_regions.pl  1.1  8 years  parrello  New script to find intergenic regions.
svr_is_hypo.pl  1.3  7 years  overbeek  minor fixes
svr_just_ends.pl  1.3  7 years  redwards  increasing min length to 2000 so that you have two ends!
svr_keep_only.pl  1.1  8 years  overbeek  support filtering on function or role
svr_kill_RAST_job.pl  1.4  8 years  olson  fix usage message
svr_link_to_compare_regions.pl  1.4  7 years  fangfang  fixed typo in $genomeH
svr_location_of.pl  1.2  4 years  parrello  CDMI and Sprout load fixes. Locations fixes.
svr_make_pan_genome_prot_families.pl  1.10  6 years  overbeek  fix bad comments
svr_mapped_genomes.pl  1.4  7 years  parrello  Fixed a leftover hack.
svr_mark_tree_states.pl  1.5  5 years  golsen  Fix my comments on rendering.
svr_md5_of_prot.pl  1.4  6 years  overbeek  get rid of debugging statement
svr_members_of_otu.pl  1.4  5 years  overbeek  add entry for rep
svr_metabolic_reconstruction.pl  1.5  8 years  olson  bah, fix paste error
svr_missing_roles.pl  1.2  7 years  overbeek  added -g genome
svr_motif.pl  1.4  7 years  fangfang  simplify code
svr_neighborhood_of_role.pl  1.3  7 years  parrello  Converted to use chemistry data instead of the models.
svr_neighboring_reactions.pl  1.2  7 years  overbeek  minor fixes
svr_neighbors_of.pl  1.5  3 years  overbeek  error checking
svr_oligomer_similarity.pl  1.1  8 years  overbeek  compute oligo similarities
svr_otus.pl  1.3  8 years  overbeek  minor fixes
svr_pegs_in_subsystems.pl  1.7  7 years  parrello  Fixed to process 10 subsystems at a time, reducing the chances of a timeout.
svr_pegs_with_evcode.pl  1.2  7 years  overbeek  must have genomes specified
svr_possible_joins.pl  1.1  8 years  overbeek  tools to try to bridge contigs
svr_preferred_roles.pl  1.6  3 years  overbeek  translation fixes
svr_project_by_sr.pl  1.1  5 years  overbeek  project with SRs
svr_project_model.pl  1.2  6 years  overbeek  effectors are not required input
svr_protein_assertions.pl  1.6  8 years  disz  CHanged ACHserver to SAPserver and fixed processing of return values
svr_psiblast_search.pl  1.28  4 years  fangfang  add core seed db
svr_put_set.pl  1.1  7 years  disz  New persistent set svr scripts
svr_quick_assign.pl  1.3  4 years  olson  Add tempdir()/tempfile() calls to manage create temps in right place. Add status...
svr_rRNA.pl  1.2  7 years  fangfang  update pod
svr_reaction_description.pl  1.3  7 years  parrello  Added -f flag.
svr_reaction_gain_loss_table.pl  1.1  5 years  golsen  Tools for mapping reaction presence and absence onto a tree.
svr_reactions_in_model.pl  1.1  7 years  parrello  New script for Ross.
svr_reactions_to_roles.pl  1.1  7 years  parrello  New chemistry-based scripts.
svr_regulons_to_fids.pl  1.1  6 years  parrello  New script to get the features in a regulon.
svr_representative_sequences.pl  1.2  4 years  fangfang  add -a n_thread option
svr_reroot_tree.pl  1.3  8 years  overbeek  fix typo
svr_retrieve_RAST_job.pl  1.3  9 years  olson  Misc server fixes
svr_role_to_complex.pl  1.1  6 years  parrello  New script to map roles to complexes.
svr_role_to_pegs.pl  1.3  7 years  overbeek  mispelled genome with bad consequences
svr_roles_to_reactions.pl  1.2  5 years  overbeek  get reactions implied by roles
svr_roles_to_subsys.pl  1.3  3 years  redwards  changing the separator in SS classifcations
svr_run_RAST_jobs.pl  1.7  7 years  olson  Add kmerDataset selection support.
svr_scanN.pl  1.1  7 years  overbeek  scanning utilities
svr_scanP.pl  1.2  7 years  overbeek  add a little documentation
svr_scripts.t  1.2  8 years  olson  updated tests
svr_seed_to_embl.pl  1.2  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
svr_seed_to_genbank.pl  1.3  2 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
svr_seed_to_table.pl  1.3  7 years  gdpusch  Fixed typo in POD section.
svr_sets_by_owner.pl  1.1  7 years  disz  enumerate sets by owner
svr_similar_to.pl  1.2  8 years  parrello  Fixed POD errors.
svr_sims2html.pl  1.6  8 years  golsen  Add pod documentation.
svr_sketch_tree.pl  1.4  7 years  golsen  Trivial change to the usage information.
svr_sphinx_indexing.pl  1.1  4 years  overbeek  add access to sphinx indexes
svr_split_fams.pl  1.1  7 years  overbeek  minor changes
svr_spreadsheet_to_file.pl  1.2  7 years  disz  Fixed missing file error message
svr_ss_classes.pl  1.1  7 years  parrello  Added to get classification data for subsystems.
svr_status_of_RAST_job.pl  1.4  8 years  olson  add url argument
svr_submit_RAST_job.pl  1.17  2 years  olson  Add rasttk submission support
svr_submit_correspondences.pl  1.2  7 years  parrello  Enhanced to handle Ross's alternate directory structure for correspondence maps....
svr_subsystem_classification.pl  1.1  7 years  gdpusch  Initial prototype checkin, still missing bells and whistles.
svr_subsystem_genome_data.pl  1.1  8 years  parrello  More server scripts.
svr_subsystem_genomes.pl  1.1  8 years  parrello  Discrimination functions support scripts.
svr_subsystem_roles.pl  1.2  7 years  overbeek  allow ss from stdin
svr_subsystem_spreadsheet.pl  1.1  8 years  parrello  subsystem download scripts.
svr_subsystems_to_roles.pl  1.1  4 years  overbeek  get roles of subsystems
svr_summarize_MG_output.pl  1.4  8 years  overbeek  extend the number of digits in the fraction of the total
svr_summarize_contigs.pl  1.2  8 years  parrello  New script, some documentation fixes.
svr_summarize_protein_families.pl  1.2  7 years  overbeek  minor changes
svr_tab2html.pl  1.5  8 years  gdpusch  Fixed a bug I introduced, and added a "--border" option to the table.
svr_taxonomically_related_genomes.pl  1.10  7 years  fangfang  update POD
svr_taxonomy.pl  1.4  6 years  fangfang  Added flag for taxonomy level
svr_tips_of_tree.pl  1.2  8 years  overbeek  add correspondence translation
svr_tmpred_predictions.pl  1.2  5 years  overbeek  fix_comment
svr_translations_of.pl  1.6  7 years  golsen  Add an option of genome names in the output. Clean up the way functions are adde...
svr_tree.pl  1.10  7 years  fangfang  add parallel support for bootstrap
svr_tree_to_html.pl  1.14  3 years  fangfang  add fetch_seed_gto.pl
svr_trim_ali.pl  1.10  7 years  fangfang  fix description field in trim html
svr_update_assignments.pl  1.3  8 years  gdpusch  Fixed typo.
svr_update_corr_maps.pl  1.2  7 years  overbeek  minor fix
svr_upstream.pl  1.9  4 years  parrello  CDMI and Sprout load fixes. Locations fixes.
svr_which_genus_species.pl  1.1  5 years  overbeek  basic kmer validation tools
svr_with_close_blast_hits.pl  1.1  7 years  overbeek  a utility to find close hits
sync_new_system.pl  1.6  12 years  golsen  Just adding a newline at end of file to make repository match my working copy. ...
synchronize_annotations_and_assignments.pl  1.2  12 years  olson  Add license words.
tabs2rel.pl  1.4  3 years  parrello  Changes copied from SEEDtk project.
test_Observation.pl  1.1  11 years  mkubal  for testing
test_cv.expected  1.1  13 years  efrank   Basic regression test on CV stuff at FIG API level (which underlies CGI).
test_cv.pl  1.2  12 years  olson  Add license words.
test_figfam_FF_peg.pl  1.3  10 years  olson  Missed one of the figfamdata fixes.
test_figfam_peg.pl  1.6  10 years  arodri7  update changes
test_figfam_placement_into_families.pl  1.10  8 years  disz  FigFam 6 digit problem
test_generate_anno_gff.pl  1.3  12 years  olson  Add license words.
test_parse_gff.pl  1.3  12 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
test_placement.pl  1.1  11 years  overbeek  redone FIGfam stuff
tips_of.pl  1.3  11 years  overbeek  add insert_prot_into_tree, a new way to insert proteins into a tree
tmpred_predictions.pl  1.2  5 years  overbeek  version untied to Sapling
to_arabidopsis.pl  1.1  11 years  hwang  This script parses arabidopsis.org to get the AT aliases output
to_fasta.pl  1.1  6 years  overbeek  initial versions
to_genbank.pl  1.7  8 years  gdpusch  Fixed bug handling 5S.
to_gg.pl  1.2  12 years  olson  Add license words.
to_gids.pl  1.2  12 years  olson  Add license words.
to_insert.pl  1.2  12 years  olson  Add license words.
to_map_coords.pl  1.3  12 years  olson  Add license words.
to_org_specific.pl  1.4  12 years  hwang  fix syntax error
to_prodom.pl  1.7  9 years  olson  fix updated URL
to_run_daily.sh  1.4  6 years  disz  Updated to use recent_annotations_by_genome
to_run_new_genomes.sh  1.3  7 years  disz  Added source of environment
to_structured_english.pl  1.1  10 years  overbeek  add routine to build structured english rendering of evidence codes
trace.pl  1.3  10 years  parrello  Fixed so that the destination is not case-sensitive.
track_figfams.pl  1.2  12 years  overbeek  get rid of diagnostics in track_figfams
trail.pl  1.1  6 years  disz  New scripts to load the function audit trail database
translate.pl  1.2  12 years  olson  Add license words.
translate_fasta.c  1.1  6 years  golsen  Support for codon usage analyses.
translate_fasta_6.c  1.2  3 years  golsen  Fixed issues in correctly printing the descriptions.
translation_of.pl  1.2  12 years  olson  Add license words.
trim_alignment.pl  1.2  11 years  overbeek  minor fixes
trim_sequences.pl  1.11  9 years  overbeek  fixes bug in handling multidomain prots
trimmed_kernel_alignment.pl  1.1  11 years  overbeek  add last round of phylogeny tools
uni_lit_to_dlits.pl  1.1  10 years  overbeek  dlit support
uninstall.pl  1.2  12 years  olson  Add license words.
uninstall.sims.pl  1.2  12 years  olson  Add license words.
update-caches.pl  1.1  11 years  olson  Update SEED caches.
update_FIGfams.pl  1.12  9 years  arodri7  commit changes
update_OTUs.pl  1.5  7 years  overbeek  fix OTU update to use gary olsen sequence grouping script
update_PSEED_subsystems.pl  1.3  8 years  olson  add doc
update_SSU_rRNAs.pl  1.1  9 years  overbeek  update of SSUs
update_fr2go.pl  1.1  11 years  overbeek  put in the fr2go stuff
update_hope_info.pl  1.4  8 years  dejongh  added comments
update_kegg_data.pl  1.6  8 years  dejongh  removed comment
update_lineage.pl  1.3  10 years  wilke  draft version to update FIG taxonomy entries
update_nr_cycle.pl  1.6  12 years  overbeek  load ext org table on update_nr_cycle
update_phage_annotations.pl  1.1  5 years  redwards   a set of scripts for adding phage genomes to the seed
update_sims.pl  1.13  12 years  olson  Add license words.
update_sims2.pl  1.6  8 years  olson  updated code
update_taxonomies.pl  1.9  21 months  olson  Revamp of this script to use efetch utility instead of parsing webpage and to ta...
update_uniq_id_data.pl  1.7  11 years  olson  use function_of_quick
uproot.pl  1.1  11 years  overbeek  add uproot
upstream.pl  1.3  12 years  olson  Add license words.
valid_fasta_file.pl  1.1  8 years  olson  Check to ensure a fasta file is valid.
validate_fasta.pl  1.1  11 years  redwards  Initial release of programs to check and fix valid fasta format
validate_genome_gff.pl  1.6  12 years  olson  Add license words.
validate_subsystem.pl  1.2  12 years  olson  Add license words.
verify_genome_directory.pl  1.44  6 months  olson  fix warning output
verify_pegs_in_tbl.pl  1.2  12 years  olson  Add license words.
wb.pl  1.1  8 years  overbeek  workbench for alignments and trees
weak_predictors.pl  1.1  4 years  overbeek  annotate via families and weak predictors
where_does_seq_hit.pl  1.2  12 years  olson  Add license words.
where_shifts_occurred.pl  1.2  5 years  overbeek  fix child check
write_go_mappings.pl  1.4  4 years  olson  Specialty protein & PATRIC caller code.

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