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File Rev. Age Author Last log entry
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BuildCodonUsageExchAndLoadFiles.pl  1.1  5 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  5 years  overbeek  allow option to preserve sequence order
CSA_close_strains.pl  1.8  6 years  overbeek  sort space in this directory
CSA_collapse_repeats.pl  1.3  6 years  overbeek  make sorts in local dir, not /tmp
CSA_create_SNP_data.pl  1.7  4 years  overbeek  compute correspondences for a pan genome
CSA_filter_unique.pl  1.2  6 years  overbeek  make part of myRAST distribution
CSA_first_pass.pl  1.4  6 years  overbeek  remove dependency on BasicLocation
CSA_gather_mapped_objects.pl  1.2  6 years  overbeek  make part of myRAST distribution
CSA_get_close_strain_annotations.pl  1.5  6 years  overbeek  spelling errors
CSA_get_repeat_dna.pl  1.2  6 years  overbeek  make part of myRAST distribution
CSA_layout.pl  1.2  6 years  overbeek  make part of myRAST distribution
CSA_make_conn.pl  1.2  6 years  overbeek  make part of myRAST distribution
CSA_make_contig_index.pl  1.2  6 years  overbeek  make part of myRAST distribution
CSA_make_unique_kmers.pl  1.4  6 years  overbeek  make sorts in local dir, not /tmp
CSA_merge_estimates.pl  1.8  6 years  overbeek  add translations to features
CSA_predict_features_based_on_refs.pl  1.1  6 years  overbeek  minor fixes
CSA_ref_vs_ref.pl  1.6  5 years  overbeek  extra comments
CSA_second_pass.pl  1.4  6 years  overbeek  fix coordinates within alignments
CS_build_fasta_for_phylogeny.pl  1.6  3 years  overbeek  take gids from genome.names
CS_compute_coupling.pl  1.5  3 years  overbeek  take gids from genome.names
CheckCELfiles.R  1.1  7 years  olson  R script to find chip name from CEL files
Consistency_Families.pm  1.1  9 years  bartels  *** empty log message ***
EcoliRMA.R  1.2  7 years  overbeek  from Matt
EmergencyMapFlipper.pl  1.2  7 years  parrello  *** empty log message ***
EmergencySubsystemFix.pl  1.2  6 years  parrello  Bug fix in index_subsystems call.
FFB2_build_ff_indexes.pl  1.1  7 years  olson  Rollup of figfam update fixes
FFB2_build_updated_FF.pl  1.24  4 years  olson  Update to figfam processing
FFB2_compare_tests.pl  1.4  6 years  olson  Update to figfam build code
FFB2_compare_to_anno3.pl  1.2  7 years  olson  fixes for release names
FFB2_compute_relationships_for_genera.pl  1.1  7 years  olson  New FIGfam merge code.
FFB2_create_binary_kmers.pl  1.6  6 years  olson  Update to figfam build code
FFB2_create_binary_relationships.pl  1.1  7 years  olson  New FIGfam merge code.
FFB2_families_in_subsystems.pl  1.1  7 years  olson  Update to FF processing
FFB2_genome_group_pipeline.pl  1.1  7 years  olson  New FIGfam merge code.
FFB2_get_oligos.pl  1.10  7 years  disz  FigFam 6 digit problem
FFB2_get_oligos2.pl  1.4  4 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  7 years  olson  Bunch of figfam generation optimizations.
FFB2_install_kmers.pl  1.2  7 years  olson  Update to FF processing
FFB2_load_memcache.pl  1.7  6 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  4 years  olson  Update to figfam processing
FFB2_make_family_vector.pl  1.1  6 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  4 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  7 years  olson  Update to FF processing
FFB2_pull_extreme_FF_members.pl  1.2  4 years  olson  Update to figfam processing
FFB2_run_tests.pl  1.3  6 years  olson  Update to figfam build code
FFB2_split_fams_by_size.pl  1.3  23 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
FFB2_update_FIGfams.pl  1.17  4 years  olson  Update to figfam processing
FFB2_usable_motifs.pl  1.4  7 years  olson  Update to FF processing
FFB2_usable_motifs2.pl  1.3  6 years  olson  Update to figfam build code
FFB2_validate_families.pl  1.1  7 years  olson  Update to FF processing
FFB2_xx.pl  1.1  7 years  olson  Bunch of figfam generation optimizations.
FFB2_xy.pl  1.1  7 years  olson  Update to FF processing
FFB3_assemble_translations.pl  1.2  4 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_build_ff_indexes.pl  1.1  5 years  olson  New figfam building code.
FFB3_build_ff_oligos.pl  1.1  5 years  olson  New figfam building code.
FFB3_build_otu_oligos.pl  1.1  5 years  olson  New figfam building code.
FFB3_build_updated_FF.pl  1.5  4 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_cleanup_families.pl  1.1  4 years  olson  Favor non-blank functions in FFB3_update_FIGfams::function_of_family Add new scr...
FFB3_compare_tests.pl  1.1  5 years  olson  New figfam building code.
FFB3_construct_assigned_functions.pl  1.2  4 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_create_binary_kmers.pl  1.1  5 years  olson  New figfam building code.
FFB3_families_to_fasta.pl  1.1  5 years  olson  New figfam building code.
FFB3_get_gs_oligos.pl  1.1  5 years  olson  New figfam building code.
FFB3_get_oligos.pl  1.1  5 years  olson  New figfam building code.
FFB3_get_recent_annotations.pl  1.2  4 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_load_oligo_index.pl  1.1  5 years  olson  New figfam building code.
FFB3_make_subsys_based_families.pl  1.2  4 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  5 years  olson  New figfam building code.
FFB3_merge_and_build_kmers.pl  1.1  5 years  olson  New figfam building code.
FFB3_merge_families_by_kmers.pl  1.1  5 years  olson  roundup of figfam build changes
FFB3_package_figfams.pl  1.1  5 years  olson  New figfam building code.
FFB3_run_parallel_usable_motifs.pl  1.1  5 years  olson  New figfam building code.
FFB3_run_tests.pl  1.1  5 years  olson  New figfam building code.
FFB3_set_figfam_functions.pl  1.2  4 years  olson  Update to figfam processing
FFB3_update_FIGfams.pl  1.2  4 years  olson  Favor non-blank functions in FFB3_update_FIGfams::function_of_family Add new scr...
FFB3_usable_motifs.pl  1.1  5 years  olson  New figfam building code.
FIGMODELscheduler.pl  1.3  7 years  chenry  Switched over the PPO as the system for holding the job queue tables.
GTO_to_PGF_genome_stats.pl  1.1  9 months  jdavis  Adding GTO_to_PGF_genome_stats.pl
GeneSet_P_Values.R  1.3  6 years  dejongh  fixes
GenomeTypeObject.t  1.1  2 years  olson  Initial genome type object tester
LigandCleanup.pl  1.2  9 years  parrello  Removed obsolete use clases.
ListLits.pl  1.1  9 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  9 years  parrello  Removed obsolete use clauses.
OneShotAttributeAdder.pl  1.2  9 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  9 years  parrello  Test script for backfill.
Pipeline.R  1.4  6 years  olson  Update to expression pipeline code
README  1.1.1.1  14 years  efrank   import
RunRMA.R  1.5  6 years  dejongh  preallocate no_match_pm_mm; delete no_match row at end
RunRMA_SIF_format.R  1.1  6 years  olson  SIF-processing run-rma.
SStest.pl  1.1  3 years  parrello  CDMI and Sprout load fixes. Locations fixes.
ShewanellaRMA.R  1.1  7 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  9 years  parrello  Added for testing the Confess method.
SplitGeneSets.R  1.2  6 years  olson  Update to expression pipeline code
SwissProtJSON_to_loadfile.pl  1.1  17 months  golsen  Create wrapper program SwissProtXML_to_JSON for the XML to JSON; includes abilit...
SwissProtXML_to_JSON.pl  1.1  17 months  golsen  Create wrapper program SwissProtXML_to_JSON for the XML to JSON; includes abilit...
TestLocations.pl  1.8  9 years  parrello  Converted to use new name for Contrain method.
Tracer.pl  1.1  9 years  parrello  New script used to route STDERR messages to the trace log.
TransactFeatures.pl  1.20  9 years  parrello  Removed obsolete use clause.
WebAppBackend.pl  1.2  8 years  jared  make user and org commands case insensitive
WikiMaker.pl  1.6  9 years  parrello  Added more trace messages.
accumulate_pegs_to_scenario_paths.pl  1.1  6 years  dejongh  determine which pegs in an organism are involved in which scenario paths
aclh.pl  1.11  9 years  paarmann  added new parameter to dump contribs
aclh_reload_contrib.pl  1.2  8 years  wilke  added db handle in ach call
add_assertions_of_function.pl  1.39  4 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  10 years  redwards  just a simple attribute loader
add_close_genes.pl  1.2  12 years  olson  Add license words.
add_dlits.pl  1.1  6 years  parrello  New script for adding protein-based Dlits.
add_figbar_and_genome_attributes.pl  1.1  10 years  mkubal  v1
add_phage_from_rast.sh  1.1  4 years  redwards   a set of scripts for adding phage genomes to the seed
add_prots_to_tree.pl  1.1  10 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  9 years  disz  Added escape arg to structured engkish
add_to_alignment.pl  1.8  6 years  golsen  Fix the libraries used for I/O.
add_to_subsystems.pl  1.1  11 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  10 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  1.3  7 years  golsen  Add support for alignment with muscle.
align_seqs.pl  1.1  10 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  10 years  golsen  Trivial format change.
alignment_to_html.pl  1.4  5 years  golsen  Add more flexible color by residue: -R ale | default | gde | none
all_bbhs.pl  1.16  10 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  6 years  parrello  Added CSV output that can be used to generate a spreadsheet of recommended funct...
analyze_package_logs.pl  1.1  5 weeks  parrello  Changes copied from SEEDtk project.
analyze_scenario_connections.pl  1.4  9 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  6 years  disz  Check in coming dates
apply_annotations.pl  1.7  3 years  olson  Fix in the case of an empty skiplist.
apply_automatic_subsystem_updates.pl  1.1  6 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  11 years  overbeek  fixes to extract_genomes
assemble_selected.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
assess_completeness.pl  1.9  9 years  gdpusch  Fixed leading-whitspace bug.
assess_gene_call_quality.pl  1.14  7 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  8 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  11 years  overbeek  fixes to Assignments.pm
assign_to_dna_using_kmers.pl  1.6  5 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  9 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  8 years  arodri7  commit changes
assign_using_ff_original.pl  1.1  8 years  arodri7  original format of assign_using_ff
assign_using_ff_parallel.pl  1.2  8 years  arodri7  made updates to functions used for updating FIGfams
assign_using_kmers.pl  1.8  7 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  5 years  redwards  adding code to make an assigned_functions file in rast dirs
at.pl  1.3  6 years  fangfang  update
auto_assign.pl  1.19  9 years  olson  Add -orgdir option to use FIGV and its indexed sims.
backfill_gaps.pl  1.21  2 years  gdpusch  Accept as few as a single template if it is in a subsystem.
backup_critical_data.pl  1.5  8 years  olson  fix bug that kept subsystems from being backedup
backup_subsystems.pl  1.3  9 years  parrello  Fixed a POD error.
bayes_expected_start_scores.pl  1.3  10 years  overbeek  Added comments to expalin logic. -- gdp
bbh_synteny.pl  1.1  2 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  10 years  overbeek  add best_tree_using_proml_on_cluster
bielefeld_tarfile_to_seed.pl  1.7  11 years  overbeek  Tweaked usage msg. -- /gdp
blast2gff.pl  1.23  7 years  redwards  adding an option for gziped files
blastP.pl  1.1  8 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  10 years  mkubal  blast pdb against nr
blast_request.pl  1.2  12 years  olson  Add license words.
blastn_chunks.pl  1.3  10 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  8 years  redwards  adding a default cutoff
blocked_by.pl  1.1  3 years  overbeek  find out why a kmer was blocked
boot_cluster_seed.pl  1.5  11 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
br_evaluate_properties.pl  1.1  4 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  10 years  overbeek  debugged version of bring_tree_up_to_ali
build_PGs_for_OTUs.pl  1.2  5 years  overbeek  fix path
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  11 years  redwards  using is_environmental
build_aligns_and_trees_for_seqs.pl  1.2  5 years  fangfang  removed comments
build_all_prok_seqs.pl  1.1  7 years  overbeek  get all protein sequences for complete prokaryotic genomes
build_anno_clearinghouse.pl  1.6  9 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
build_contigs_blastdb.pl  1.1  21 months  olson  New blastdb builders.
build_dnaseq_blastdb.pl  1.1  21 months  olson  New blastdb builders.
build_dtr_distro.pl  1.4  6 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  1.2  4 months  olson  fixes
build_figfam_pssm_db.pl  1.2  10 years  gdpusch  Major modifications to &load_family_ids()
build_initial_objects_for_start_predictions.pl  1.12  9 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  7 years  disz  FigFam 6 digit problem
build_nohit_fasta.pl  1.2  12 years  olson  Add license words.
build_nr.pl  1.22  9 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
build_nr_md5.pl  1.1  4 years  olson  md5 nr builder
build_nr_sources.pl  1.14  10 years  olson  Rollup of various rast-related changes.
build_partition_index.pl  1.1  9 years  overbeek  return empty list of failure to open FIFfam
build_prok_nonff_fasta.pl  1.4  7 years  disz  FigFam 6 digit problem
build_protein_families.pl  1.5  12 years  olson  Add license words.
build_sas_distro.pl  1.11  6 years  devoid  Making changes to build distro to support ModelSEED packages. Modified Files: F...
build_sas_distro_from_cvs.pl  1.5  6 years  olson  Revert to the versions from backups.
build_sets_from_clusters.pl  1.2  6 years  parrello  Minor fixes for debugging.
build_solid_set.pl  1.3  4 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  8 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  7 years  olson  fix ANNOserver args
call_genome_using_glimmer.pl  1.4  23 months  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  8 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  10 years  olson  Missing scripts.
check_figfams.pl  1.6  9 years  olson  Introduct &FIG::get_figfams_data()
check_for_new_genomes.pl  1.3  8 years  overbeek  print stats as you go
check_for_possible_mobile_elements.pl  1.1  10 years  overbeek  add code to search for mobile elements
check_for_scenario_reachability.pl  1.3  9 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  4 years  overbeek  handle dup assignments
check_hope_info.pl  1.8  7 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  9 years  dejongh  switch to scenario_directory
check_model_v2.pl  1.2  9 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  10 years  overbeek  redone FIGfam stuff
check_rast.pl  1.1  5 months  parrello  Changes copied from SEEDtk project.
check_sims_basic.pl  1.8  11 years  redwards  using is_environmental instead of seven 9s
check_sims_for_added_genome.pl  1.1  4 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  9 years  overbeek  minor fix to handle deleted subsystems
check_subsystems.pl  1.7  10 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  2 weeks  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  8 years  arodri7  commit changes
close_connections.pl  1.2  10 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  7 years  overbeek  cluster experiments into states
cluster_objects.pl  1.9  2 years  overbeek  hande connections between identical keys
clustered_hypotheticals.pl  1.2  7 years  overbeek  major rewrite
codon_counts_x_and_p.c  1.1  5 years  golsen  Support for codon usage analyses.
codon_freq_eval_2.c  1.1  5 years  golsen  Support for codon usage analyses.
collect_related_sequences.pl  1.3  10 years  golsen  Encapsulate all of the SEED-dependent functions in the perl module. It should st...
compareMR.pl  1.1  10 years  overbeek  basic stuff for comparing metabolic reconstructions
compare_annotation_sets.pl  1.1  3 years  olson  Annotation comparison tool.
compare_ec_gary_table.pl  1.1  2 years  redwards  module and scripts to compare EC numbers to what we have in the SEED
compare_figfam_release_results.pl  1.5  8 years  arodri7  commit changes
compare_gto_assigned_roles.pl  1.1  3 years  gdpusch  Initial checkin.
compare_gto_called_CDSs.pl  1.1  3 years  gdpusch  Initial checkin.
compare_scenarios.pl  1.5  9 years  dejongh  Changes to move the 'All' scenarios directory to FIG_Config::global/Models/All
compare_tbls.pl  1.5  11 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  8 years  overbeek  stuff for gene calling
complement_fasta.c  1.1  5 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  10 years  mkubal  test for dir exist
compute_PCA_for_metagenomes.pl  1.1  8 years  mkubal  called by PCA_ssav
compute_PCA_with_metagenomes_as_variables.pl  1.1  8 years  mkubal  called by PCA_mgav
compute_PSEED_reconstructions.pl  1.2  6 years  olson  More fixups.
compute_atomic_regulons.pl  1.3  4 years  overbeek  compute correspondences for a pan genome
compute_atomic_regulons_for_dir.pl  1.2  6 years  overbeek  loosen threshhold of mismatches
compute_changed_ids_for_nrs.pl  1.5  8 years  olson  misc fixes
compute_contig_md5.pl  1.4  10 years  olson  rollup of metagenome server changes
compute_crc64_for_all_pegs.pl  1.1  10 years  mkubal  v1
compute_dbdir_checksum.pl  1.3  11 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
compute_ev_code_attributes.pl  1.2  9 years  overbeek  do not include cluster-based subsystems in forming evidence codes
compute_extra_dlit_data.pl  1.4  9 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
compute_fasta_lengths.pl  1.1  7 years  olson  Precompute fasta lengths for the non-FF nr.
compute_figfam_assignments.pl  1.2  7 years  olson  Clean up debugging, write concatenated output file.
compute_genome_counts.pl  1.25  8 years  olson  Fix bug where compute_genome_counts fails to run on a genome directory with mult...
compute_genome_similarity.pl  1.1  10 years  olson  Missing scripts.
compute_mw_and_pi.pl  1.2  10 years  mkubal  one genome at a time
compute_mw_and_pi_with_BioPerl.pl  1.1  10 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  4 years  overbeek  compute correspondences for a pan genome
compute_pchs_from_sims.pl  1.2  10 years  olson  Rollup of changes for the new RAST install.
compute_pins.pl  1.4  9 years  olson  undo bogus commit
compute_pins_and_clusters.pl  1.2  12 years  olson  Add license words.
compute_potential_fusions.pl  1.12  11 years  overbeek  fix to fusions
compute_ribo_ratio.pl  1.1  4 years  overbeek  quality control using ribo proteins
compute_ribo_ratio_by_function.pl  1.1  4 years  overbeek  quality control using ribo proteins
compute_sim_chunk.pl  1.3  11 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  3 years  overbeek  handle a strange floating point issue
compute_translation_MD5.c  1.3  6 years  redwards  ignoring stops
condense_blast.pl  1.2  12 years  olson  Add license words.
condense_kmer_output.pl  1.2  3 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  9 years  arodri7  update changes
connect_PDB_to_FIGfams_worker.pl  1.1  9 years  arodri7  update changes
connections_between.pl  1.8  8 years  overbeek  fixes to making close strain data
convert-blast-to-m8.pl  1.1  8 years  olson  Convert full blast output to -m8 output using Gary's blast parsing code.
convert_tbl_files.pl  1.1  6 years  parrello  New script for fancy tbl file conversion.
core_PGF_stats.pl  1.1  9 months  jdavis  Adding core_PGF_stats.pl
corr_build_connections.pl  1.1  6 years  parrello  New stuff for Salmonella sets.
correct_frameshifts.pl  1.26  5 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  9 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  9 years  bartels  *** empty log message ***
create_ff_covering_skeleton.pl  1.3  5 years  overbeek  remove invocation of representative_sequences
create_sims_btree.pl  1.1  11 years  olson  BTREE-index versions of these. Experimental still.
cripple_gto.pl  1.1  9 months  parrello  Changes copied from SEEDtk project.
cs_adjacency_data.pl  1.6  2 years  overbeek  fix tmp on sort
curator_of.pl  1.1  11 years  overbeek  minor fixes to assignment for close strains
daily.pl  1.9  5 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  11 years  overbeek  RAE: New delete attribute files to remove all files. maybe this will work
delete_fids_from_orgdir.pl  1.2  11 months  gdpusch  Improved command-line argument processing
delete_functions_for_nonextent_ff.pl  1.1  4 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  23 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
difference_between_two_databases.pl  1.1  8 years  redwards  code for generating the delta between two databases
direct_functional_coupling.pl  1.4  10 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.
dp.pl  1.4  8 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  4 years  redwards   a set of scripts for adding phage genomes to the seed
ec_compare_sib.pl  1.1  2 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  10 years  olson  generate feature registration stuff
estimated_fabric.pl  1.1  8 years  overbeek  code for processing fabrics and population estimates
ev_code_cron.pl  1.16  9 years  parrello  Updated comments to mention the replacement scripts.
evaluate_annotation_consistency.pl  1.1  4 years  fangfang  script for evaluating annotation consistency
evaluate_properties.pl  1.1  4 years  overbeek  a tool that uses boolean evaluation
evaluate_quality_of_trees.pl  1.4  10 years  overbeek  debugged version of bring_tree_up_to_ali
ex_add_conditions.pl  1.1  4 years  overbeek  add conditions/samples
ex_adjust_peg_on_off.pl  1.1  4 years  overbeek  expression pipeline + ato,ic regulons
ex_compute_pccs.pl  1.3  4 years  overbeek  add spearman stuff
ex_fillout_ar_data.pl  1.1  4 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  4 years  overbeek  get locus/peg right
ex_pipeline_ross.pl  1.5  3 years  overbeek  added some documentation
ex_rare_ar_and_pegs.pl  1.1  4 years  overbeek  added steps
ex_set_on_off_for_atomic_regulons.pl  1.1  4 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  9 years  parrello  Fixed a POD error.
exec-cgi.pl  1.1  7 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  9 years  olson  *** empty log message ***
expand_transferred_chunks.pl  1.4  12 years  olson  Add license words.
explore_subsys_pmid.pl  1.5  10 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  9 years  overbeek  fixes relating to comments
export_all_viruses.pl  1.1  4 years  redwards   a set of scripts for adding phage genomes to the seed
export_dlits.pl  1.2  9 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  4 years  redwards  a cron job to export phage data
export_similarity_request.pl  1.3  11 years  overbeek  minor fixes to assignment for close strains
export_subsystem.pl  1.1  18 months  olson  Subsystem exporter for NCBI.
export_subsystem_as_gff.pl  1.2  12 years  olson  Add license words.
extend_subsys.pl  1.7  11 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  8 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  11 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  11 years  overbeek  changes to support dynamic sims and updates
extract_genomes_from_samples.pl  1.2  4 years  overbeek  needs work on getting rRNAs
extract_halo_genomes.pl  1.7  4 years  overbeek  compute correspondences for a pan genome
extract_metagene_contigs.pl  1.12  7 years  gdpusch  Updated search for executables to revised software environment.
extract_sp_links.pl  1.3  11 years  olson  fix -h error
extract_subset_from_sprout_data.pl  1.2  12 years  olson  Add license words.
fabric_vec.pl  1.1  8 years  overbeek  add ability to make fabric vecs
fast_blastp.pl  1.1  9 years  overbeek  fast_blastp is a tool to support rapid similarity estimates using FIGfam partiti...
fast_grep.pl  1.1  4 years  overbeek  example of systead
fast_project.pl  1.3  2 years  olson  bugfix
fast_project_ref_to_GTO.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
fasta_cksum.c  1.4  12 years  olson  Doh, put proper comments in for C code.
fasta_for_hypo.pl  1.2  12 years  olson  Add license words.
fasta_size.pl  1.1  8 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  7 years  disz  FigFam 6 digit problem
feature_length_histogram.pl  1.4  23 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
features_with_role.pl  1.1  10 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  6 years  fangfang  initial import
fetch_seed_gto.pl  1.4  2 years  parrello  Changes copied from SEEDtk project.
ff.pl  1.7  7 years  disz  FigFam 6 digit problem
fid2dna.pl  1.2  12 years  olson  Add license words.
fig.pl  1.157  2 years  overbeek  add change_funcrole
fig_net.pl  1.4  9 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
fig_rpc.pl  1.4  9 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
fig_specific_sequences.pl  1.3  11 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  7 years  disz  FigFam 6 digit problem
figfam_quality_control.pl  1.8  8 years  arodri7  commit changes
figfam_size_distribution.pl  1.1  9 years  arodri7  update changes
figfam_subsystems.pl  1.2  8 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  6 years  overbeek  merge is better
filter_codon_counts.pl  1.1  5 years  golsen  Support for codon usage analyses.
filter_figfams.pl  1.2  10 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  7 years  overbeek  filter pegs with no raw data
filter_overlaps.pl  1.5  11 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  11 years  overbeek  set up find_neighbors to handle existing genomes
filter_trunc_and_fs.pl  1.2  7 years  olson  Add SeedUtils::map_to_families for iterating over families.2c files. Make filte...
find_IS.pl  1.8  3 years  olson  add sas tag
find_RNA_genes.pl  1.1  2 years  golsen  Make blast+ the default in find_nucleotide_homologs, solving an issue with occas...
find_SEED_SSU_rRNA_genes.pl  1.7  4 years  golsen  Update the reference RNA module name.
find_approx_neigh.pl  1.7  6 years  gdpusch  Added debugging info on number and types of conserved proetins found.
find_bad_conflicts.pl  1.1  11 years  overbeek  fixes to wseekly statistics
find_bad_contigs.pl  1.1  13 months  parrello  Changes copied from SEEDtk project.
find_bidir_best_hits.pl  1.1  3 years  fangfang  import Gary's find_bidir_best_hits script
find_close_genomes.pl  1.2  22 months  parrello  Changes copied from SEEDtk project.
find_essential_reactions.pl  1.3  9 years  dejongh  switch to scenario_directory
find_gaps.pl  1.9  8 years  gdpusch  Fixed (hopefully) incorrectly handled out-of-bounds cases.
find_genes_based_on_kmers.pl  1.9  6 years  olson  More fixups.
find_genes_based_on_neighbors.pl  1.24  8 years  olson  Switch to FFs and FF instead of FigFams and FigFam
find_genes_based_on_neighbors_par.pl  1.1  7 years  olson  parallel version of find_genes_based_on_neighbors
find_genes_in_families.pl  1.22  8 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  23 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
find_missing_genes.pl  1.10  7 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  9 years  dejongh  switch to scenario_directory
find_missing_lib_inputs_v2.pl  1.2  9 years  dejongh  switch to scenario_directory
find_model_cofactors.pl  1.7  9 years  dejongh  switch to scenario_directory
find_model_information.pl  1.7  9 years  dejongh  switch to scenario_directory
find_model_information_v2.pl  1.2  9 years  dejongh  switch to scenario_directory
find_more_instances_for_veronika.pl  1.1  5 years  overbeek  Fangfang tools to support Veronika
find_neighbors.pl  1.39  7 years  disz  FigFam 6 digit problem
find_neighbors_by_sim.pl  1.4  9 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
find_neighbors_using_figfams.pl  1.11  8 years  olson  Switch to FFs and FF instead of FigFams and FigFam
find_new_annotations.pl  1.6  4 years  parrello  Fixed to recover from genomes with missing annotation files.
find_poss_errs.pl  1.3  7 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  23 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
find_rnas.pl  1.2  7 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  9 years  gdpusch  Suppress writing "called_by" and "special_pegs" when "-keep" is selected. -- /gd...
find_subsys.pl  1.3  9 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  10 years  redwards  Initial release of programs to check and fix valid fasta format
flatten_attribute_files.pl  1.2  6 years  redwards  working on all subdirectories, not just a set of them
flatten_erdb_xml.pl  1.1  5 years  olson  script to write tabular form of ERDB XML file
flatten_fasta.pl  1.1  11 years  overbeek  add some minor utilities to flatten/unflatten fasta files
flattened_to_fasta.pl  1.1  11 years  overbeek  add some minor utilities to flatten/unflatten fasta files
flip_sims.pl  1.7  10 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
form_clusters.pl  1.2  8 years  parrello  Final Server updates.
format_partition_dbs.pl  1.2  8 years  overbeek  try
format_peg_dbs.pl  1.3  12 years  olson  Add license words.
fq_to_fa.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
freqs_2_dists.pl  1.1  5 years  golsen  Compute pairwise distances between sets of codon usage frequencies.
freqs_2_nj_tree.pl  1.3  5 years  golsen  Some minor changes.
function_of.pl  1.5  9 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
functionally_coupled.pl  1.7  9 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  8 years  olson  Add more data gathering
gather_pg_sets.pl  1.3  6 years  overbeek  minor fixes
gd_tree.pl  1.1  8 years  golsen  Add a command line program to make a png graphic from a newick tree file.
genbank2fasta.pl  1.2  8 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  8 years  overbeek  stuff for gene calling
generate_dlit_ev_codes.pl  1.5  9 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  9 years  overbeek  code relating to dlit/ilit maintenance
generate_ilits.pl  1.3  7 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  3 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  7 years  disz  FigFam 6 digit problem
generate_partitions_worker.pl  1.4  7 years  disz  FigFam 6 digit problem
generate_picked.pl  1.1  8 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  5 years  overbeek  no fields with tabs
generate_similarities.pl  1.3  9 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  10 years  golsen  Extensive modifications to allow more options, and handle large genomes by not r...
genome_set.t  1.1  3 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  11 years  redwards  Adding tools to handle essentiality data for Sveta
get_FIGfams_SS_NMPDR_stats.pl  1.1  8 years  arodri7  *** empty log message ***
get_NCBI_genome_attributes.pl  1.1  9 years  arodri7  get_NCBI_genome_attributes searches the NCBI internet sites for genome attribute...
get_ON_probes.pl  1.5  2 years  jdavis  updated joses new functional roles
get_PATRIC_AMR_data.pl  1.1  2 years  jdavis  adding get_PATRIC_AMR_data.pl
get_PATRIC_AMR_genome_list.pl  1.1  2 years  jdavis  adding get_PATRIC_AMR_genome_list.pl
get_PSEED_assignment_updates.pl  1.6  3 years  olson  Specialty protein & PATRIC caller code.
get_all.pl  1.2  4 years  disz  Fixed the example
get_all_annotations.pl  1.1  5 years  disz  New scripts to load the function audit trail database
get_all_dlits.pl  1.2  5 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  3 years  olson  Initial commit of Ross kmer compare regions code, coped from ~overbeek/Ross/Gene...
get_close_pegs_kmer_memcache.pl  1.2  3 years  olson  put hash size back appropriately
get_core_PGFs.pl  1.1  9 months  jdavis  Adding get_core_PGFs.pl
get_coupling_values.pl  1.3  7 years  overbeek  get rid of extraneous routine
get_dlit_data.pl  1.1  4 years  overbeek  exemplar code
get_dna.pl  1.6  9 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  9 years  parrello  Updated comments to mention the replacement scripts.
get_evaluation_check.pl  1.3  10 years  bartels  added option -a for showing pegs that do not match via blast
get_evaluation_check_rast_new_vs_old.pl  1.1  10 years  bartels   compare old rast with development version
get_exemplars_as_needed.pl  1.3  4 years  overbeek  minor fixes
get_fam_corr.pl  1.1  15 months  parrello  Changes copied from SEEDtk project.
get_fam_rel.pl  1.1  15 months  parrello  Changes copied from SEEDtk project.
get_families.pl  1.14  3 years  olson  Clean up tempdir.
get_families_1.pl  1.9  3 years  overbeek  handle bars in genome ids
get_families_2.pl  1.4  3 years  olson  Add tempdir()/tempfile() calls to manage create temps in right place. Add status...
get_families_3.pl  1.3  3 years  overbeek  fixed documentation
get_families_4.pl  1.9  3 years  olson  Add tempdir()/tempfile() calls to manage create temps in right place. Add status...
get_families_final.pl  1.3  3 years  overbeek  fixed documentation
get_families_kmcl.pl  1.1  7 months  olson  KMCL processing.
get_fasta_for_tbl_entries.pl  1.11  8 years  gdpusch  Modified to remove complaints about uninitialed values when TBL entry does not c...
get_figfam_funcs.pl  1.1  11 years  overbeek  add install_anticipated_functions and some FIGfam tracking stuff
get_genome_object_from_seed.pl  1.3  2 years  olson  add pseed
get_genomes_from_ncbi.pl  1.1  8 years  wilke  *** empty log message ***
get_id_mapping_for_list_of_IDs.pl  1.1  9 years  wilke  Draft version for id mapping
get_journals_for_frole.pl  1.1  10 years  hwang  Files to get journal information from PubMed
get_journals_for_org.pl  1.1  10 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  4 years  overbeek  more stringent bounds
get_long_enough.pl  1.2  12 years  olson  Add license words.
get_merged_families_2.pl  1.1  2 years  olson  Global merge code.
get_merged_families_3.pl  1.1  2 years  olson  Global merge code.
get_needed_corr.pl  1.1  5 years  overbeek  for veronika projections
get_neighbors_and_corr_to_ref.pl  1.7  7 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  8 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  5 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  10 years  hwang  update comment that this is for peg curation
get_recent_annotations.pl  1.1  5 years  overbeek  to support assigning FigFam functions
get_rid_of_small_or_too_many_per_FF.pl  1.2  4 years  overbeek  allow short prots in subsys
get_rna_features_for_calling_genes.pl  1.2  8 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  8 years  redwards  only call if not in a ss
get_subsystem_properties.pl  1.1  10 years  overbeek  minor modifications to get subsystems statistics
get_synonyms_from_ach_for_id.pl  1.2  9 years  wilke  *** empty log message ***
get_taxid_journals.pl  1.1  10 years  hwang  get journals from PMC using taxide
get_translations.pl  1.3  11 years  overbeek  get_translations can take PEG ids from STDIN
get_translations_for_genomes.pl  1.1  3 years  overbeek  get translations for a set of genomes
get_unique_kmers_for_rnaseq.pl  1.3  4 years  overbeek  take in K as a n argument
gff2Ontology.pl  1.4  12 years  olson  Add license words.
gff2ncbitab.pl  1.3  9 years  olson  add swissprot
gff2seed.pl  1.29  8 years  redwards  removing check for refseq ids
gff2tab.pl  1.5  10 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  5 years  golsen  Support for codon usage analyses.
gjocodonlib.h  1.1  5 years  golsen  Support for codon usage analyses.
gjoseqio.c  1.1  5 years  golsen  Support for codon usage analyses.
gjoseqio.h  1.1  5 years  golsen  Support for codon usage analyses.
gjoseqlib.c  1.1  5 years  golsen  Support for codon usage analyses.
gjoseqlib.h  1.1  5 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  3 years  olson  Genome set tests & database initialization script
gto_complete_check.pl  1.1  9 months  parrello  Changes copied from SEEDtk project.
gto_crisprs.pl  1.1  5 months  parrello  Changes copied from SEEDtk project.
gto_to_tbl.pl  1.2  23 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
harvest_genomes_from_samples.pl  1.1  4 years  overbeek  possibly buggy - salvaged after the fact
html_parser.py  1.2  12 years  olson  Add license words.
identify_organism.pl  1.2  8 years  olson  changes for new server stuff
iedb.pl  1.10  11 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  9 years  parrello  Fixed a POD error.
import_subsystems.pl  1.22  12 years  olson  Add license words.
index-pegsyn.pl  1.1  10 years  olson  Missing scripts.
index-pegsyn2.pl  1.1  9 years  olson  new version of pegsyn indexer that presorts data before inserting into the btree...
index_anno_clearinghouse.pl  1.3  10 years  olson  multiple id support, build fixes
index_annotations.pl  1.11  10 years  olson  bugfix
index_contig_files.c  1.5  11 years  olson  fix to work on 64-bit linux
index_contigs.pl  1.12  6 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  9 years  olson  Index scripts for FIGV accleration.
index_figv_annos.pl  1.1  9 years  olson  Index scripts for FIGV accleration.
index_genome.pl  1.1  6 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  10 years  olson  compute length btree also
index_pins.pl  1.3  11 years  olson  new pin indexer
index_sims.pl  1.12  8 years  olson  Bump id size.
index_sims_file.c  1.8  2 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  6 years  olson  add nonaux role index
index_translation_files.c  1.8  6 years  redwards  ignoring stops
index_translations.pl  1.24  7 years  olson  Add index on fileno.
index_translations_MD5.pl  1.4  8 years  olson  revert changes
indirect_functional_coupling.pl  1.5  11 years  overbeek  indirect functional coupling should not be from a PEG to itself
indirect_functional_coupling_mcauliffe.pl  1.5  11 years  overbeek  indirect functional coupling should not be from a PEG to itself
init_FIG.pl  1.13  6 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  11 years  overbeek  fixes to extract_genomes, salvage_subsystem_rows and initialize_alignments_for_s...
initialize_ann_and_ev.pl  1.4  6 years  olson  fix typo
initialize_figfams.pl  1.12  7 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  10 years  overbeek  add tree_neighbors and latest phylogeny stuff
insert_prot_into_tree.pl  1.14  10 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  9 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  9 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  10 years  olson  add option to install from a jobdir
install_partition_reps.pl  1.2  8 years  arodri7  commit change
install_partitions.pl  1.5  7 years  disz  FigFam 6 digit problem
install_rast_batch.pl  1.4  10 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  6 years  golsen  Fix the taxonomy to use NCBI full taxonomy if TAXONOMY does not exist.
just_inconsistent_sets.pl  1.1  6 years  overbeek  show inconsistyent sets
k-class-PSEED-kc.pl  1.1  2 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  2 years  jdavis  adding k-class-adaboost-classify.pl
k-class-adaboost-matrix-parallel.pl  1.1  2 years  jdavis  adding k-class-adaboost-matrix-parallel.pl
k-class-adaboost.pl  1.2  2 years  olson  Bob hacks to Jim's code
k-class-get-adaboost-tree-tips.pl  1.1  2 years  jdavis  adding k-class-get-adaboost-tree-tips.pl
k-class-get-bork-universals.pl  1.1  2 years  jdavis  This gets a set of universal proteins for a genome using blast
k-class-kc.pl  1.1  2 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  2 years  jdavis  adding k-class-representative_n_tree_tips.pl
k-class-tree-from-contig-dir.pl  1.2  2 years  jdavis  had to strip .pl file extensions in system calls
keep_good_connections.pl  1.3  4 years  overbeek  change definition of required ratio
keep_only.pl  1.2  12 years  olson  Add license words.
km_build_Data.pl  1.20  16 months  olson  Commit updates to kmer build code.
km_build_function_index.pl  1.1  4 years  overbeek  Release 1.0: see ~overbeek/Ross/LoosenedKmers/bin/Release1.0/bin
km_build_just_otu_index.pl  1.1  4 years  overbeek  Release 1.0: see ~overbeek/Ross/LoosenedKmers/bin/Release1.0/bin
km_build_kmers_part1.pl  1.2  4 years  overbeek  fix test for fI
km_build_kmers_part2.pl  1.1  4 years  overbeek  Release 1.0: see ~overbeek/Ross/LoosenedKmers/bin/Release1.0/bin
km_pick_best_hit_in_peg.pl  1.4  14 months  olson  Some readability / documentation changes.
km_process_hits_to_regions.pl  1.6  8 months  olson  Fix accumulation of weighted score bug.
kmc  1.1  2 years  jdavis  adding kmc
kmer_classifier.pl  1.1  3 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  4 years  overbeek  make frac hits for kmer a parameter
kmer_search.pl  1.26  12 months  olson  Add debug flag
kp_build_Data.pl  1.5  4 years  overbeek  handle frac better
kp_get_properties_next_round.pl  1.1  4 years  overbeek  a little script to make next properties file in iterative training
kp_process_dna_hits.pl  1.4  3 years  olson  Fix regex bug.
kp_process_hits.pl  1.7  3 years  olson  Fix regex bug.
kp_run_tests.pl  1.5  4 years  overbeek  fix pubseed flag
label_all_nodes.pl  1.2  4 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  9 years  overbeek  fixes to quotemeta characters in loading comments
load_abstract_coupling.pl  1.3  11 years  parrello  Changed to use a single-character delimiter (for compatability with PostGRES).
load_atomic_regulons.pl  1.1  6 years  olson  initial atomic regulon table loader
load_attributes.pl  1.46  6 years  redwards  changing the attribute of the genome table
load_bbhs.pl  1.15  9 years  olson  *** empty log message ***
load_bbhs_btree.pl  1.1  11 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  10 years  overbeek  tighten length constraints for figfam matching
load_coupling.pl  1.9  11 years  olson  Remove debugging.
load_coupling_btree.pl  1.1  11 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  9 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
load_ec_names.pl  1.6  8 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  9 years  olson  fix tmp file name.
load_function_transition_table.pl  1.1  5 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  9 years  olson  updates to the load_id_correspondence loader and searching code.
load_kegg.pl  1.15  7 years  dejongh  Fix KEGG location
load_kmer_peg_db.pl  1.1  3 years  olson  Initial commit of Ross kmer compare regions code, coped from ~overbeek/Ross/Gene...
load_kmers_into_memcache.pl  1.2  3 years  olson  memcache kmers code
load_links.pl  1.7  9 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  11 years  overbeek  introduce locks on features to block assignments
load_md5_alignment.pl  1.1  6 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  17 months  olson  pattyfam compute.
load_pch_pins.pl  1.2  12 years  olson  Add license words.
load_peg_mapping.pl  1.12  6 years  olson  Caching / FCGI speedup modifications.
load_pirsf.pl  1.14  11 years  overbeek  RAE: correcting load_pirsf not recognizing a firewall
load_propagation_locks.pl  1.1  4 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  11 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  8 years  olson  Wikipedia cache loader.
location_of.pl  1.2  12 years  olson  Add license words.
ma_pipeline.pl  1.15  7 years  overbeek  get rid of RMA Key
ma_pipeline_ecoli.pl  1.3  4 years  overbeek  compute correspondences for a pan genome
ma_pipeline_shewanella.pl  1.6  7 years  overbeek  fixes to pipeline
macapp_files_to_genome_dir.pl  1.2  7 years  olson  Banish cp.
maint-remove-obsolete-aliases.pl  1.1  10 years  olson  Missing scripts.
make_CDD_attributes.pl  1.2  10 years  mkubal  fix to score format
make_CELLO_and_TMPRED_attributes.pl  1.2  10 years  mkubal  changed ; to :: for key separator
make_FigFamsData.pl  1.4  11 years  overbeek  order generated FIGfams
make_IPR_PFAM_GO_attributes.pl  1.3  10 years  mkubal  fix to score format
make_MFA_tool_input.pl  1.2  9 years  dejongh  switch to scenario_directory
make_MPS_model.pl  1.7  9 years  dejongh  switch to scenario_directory
make_MPS_model_v2.pl  1.2  9 years  dejongh  switch to scenario_directory
make_Ontology_database.pl  1.3  9 years  mkubal  provides usage when no argument given
make_PATRICfams.pl  1.4  5 years  overbeek  minor fix
make_PATRICfams_collapse_md5.pl  1.2  5 years  overbeek  minor fixes
make_PDB_attributes.pl  1.2  10 years  mkubal  fix to score format
make_PFAM_HMM_derived_attributes.pl  1.2  10 years  mkubal  added date as 2nd argument
make_PG.pl  1.3  6 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  10 years  mkubal  fix to score format
make_Phobius_attributes.pl  1.2  10 years  mkubal  added date as 2nd argument
make_SBML_model.pl  1.6  9 years  dejongh  switch to scenario_directory
make_SignalP_attributes.pl  1.2  10 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  9 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  9 years  mkubal  provides usage when no argument given
make_close.pl  1.7  11 years  parrello  Fixed obsolete form of boundaries_of.
make_close_strain_data.pl  1.14  8 years  overbeek  fixes to making close strain data
make_close_strain_family_tabs.pl  1.2  11 years  overbeek  fixes to wseekly statistics
make_coreg_conjectures_based_on_subsys.pl  1.6  6 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  11 years  overbeek  RAE: Protein Families interface and construction
make_fasta_btree.pl  1.1  10 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  7 years  disz  FigFam 6 digit problem
make_figfam_tree_worker.pl  1.2  7 years  disz  FigFam 6 digit problem
make_figfams.pl  1.3  11 years  overbeek  families.2c should get current function - not family function
make_genome_dir_for_close.pl  1.11  13 months  gdpusch  second tweak to avoid $contig=0 errors.
make_go_ontology.pl  1.3  9 years  mkubal  provides usage when no argument given
make_indexes.pl  1.18  5 years  golsen  Fixed bugs that made script crash with older SEED layout.
make_initial_partition_scores.pl  1.1  8 years  overbeek  additions to support partitioning of sims
make_interpro_ontology.pl  1.3  9 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  2 years  disz  New script to create kbstyle md5's
make_kegg_files.pl  1.5  10 years  overbeek  Update parsing of NAME field to reflect change in source file. -- /gdp
make_ma_html.pl  1.2  6 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  9 years  arodri7  script makes the md5 to figfams file
make_model_spreadsheets.pl  1.2  9 years  dejongh  switch to scenario_directory
make_ncbi_files.pl  1.4  10 years  wilke  changed check for existing directories
make_neigh_joining_tree.pl  1.8  10 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  23 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
make_parallel_proml_run.pl  1.2  10 years  overbeek  add rates to phylogeny stuff
make_partition_reps.pl  1.1  8 years  overbeek  try
make_partition_repsP.pl  1.4  8 years  arodri7  commit change
make_partition_repsW.pl  1.1  8 years  overbeek  try
make_partition_reps_worker.pl  1.3  8 years  arodri7  commit change
make_pdb_ontology.pl  1.3  9 years  mkubal  provides usage when no argument given
make_peg_map_from_tbl.pl  1.3  8 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  8 years  olson  need to compute sims both directions because connections_between now uses bbhs.
make_pfam_ontology.pl  1.4  9 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  9 years  mkubal  provides usage when no argument given
make_predictor_input.pl  1.1  13 months  parrello  Changes copied from SEEDtk project.
make_predictor_input_from_gto.pl  1.1  13 months  parrello  Changes copied from SEEDtk project.
make_probes_to_genes.pl  1.8  6 years  dejongh  check for same contig when matching probe to peg
make_proml_tree.pl  1.6  10 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
make_proml_tree_0.pl  1.1  10 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
make_proposed_assignments_for_consistency.pl  1.4  11 years  overbeek  fixes to wseekly statistics
make_prosite_ontology.pl  1.3  9 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  10 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  10 years  olson  new script
make_release.pl  1.5  3 years  olson  Add ProblemSets.current symlink management.
make_scored_instances.pl  1.5  4 years  overbeek  compute correspondences for a pan genome
make_sim_part_data.pl  1.1  8 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  10 years  olson  compute_pchs_from_sims.pl
make_sims_and_fc_data.pl  1.1  8 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  10 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  4 years  overbeek  build input for Bob to display
make_subsys_based_families.pl  1.14  9 years  overbeek  do not use genomes with variants beginning with an asterisk in forming FIGfams b...
make_subsys_based_families2.pl  1.1  8 years  arodri7  commit changes
make_subsystems_from_clusters.pl  1.5  12 years  olson  Add license words.
make_supporting_predicates.pl  1.3  5 years  overbeek  handle minor issue with compound predicate
make_tf_equivalog_file.pl  1.1  9 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  9 years  overbeek  return empty list of failure to open FIFfam
make_uniprot_corr.pl  1.2  9 years  overbeek  build uniprot correspondence
map-nr-ids-to-ncbi-std.pl  1.1  9 years  olson  Script to map IDs in a SEED NR into forms acceptable to the indexed NCBI fasta p...
map_pegs.pl  1.3  11 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  9 years  olson  Actually write out the changed entries.
mark_genome_as_phage.pl  1.1  6 years  redwards  two phage specific scripts
mark_nr.pl  1.2  12 years  olson  Add license words.
mark_picked_genes.pl  1.2  8 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  2 years  golsen  Fixed spelling errors in the documentation.
match_to_genome_axes.pl  1.2  5 years  golsen  Updated to use GenomeCodonUsages.pm
match_to_genome_frequencies.pl  1.3  5 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  8 years  bartels  *** empty log message ***
merge_families.pl  1.3  10 years  overbeek  add strip comments argument on function_of
merge_gene_sets.pl  1.1  7 years  overbeek  code from Hope
merge_missing_gene_output.pl  1.3  7 years  olson  bugfix
merge_missing_sims.pl  1.1  4 years  redwards   a set of scripts for adding phage genomes to the seed
merge_peg_synonyms.pl  1.1  4 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  8 years  jared  added update_path
metagenome2genbank.pl  1.4  9 years  mkubal  includes data from meta.xml
mg_user_id_to_unique.pl  1.2  9 years  mkubal  full loop
modal_codon_usage.pl  1.2  5 years  golsen  Add full fasta description line to counts file.
modelCompare.pl  1.1  4 years  disz  Janaka reaction code
modify_tree.pl  1.1  7 years  golsen  A general purpose tree modification utility.
myjoin.pl  1.1  11 years  overbeek  fix building FigFamData
native_codon_usage.pl  1.1  5 years  golsen  Support for codon usage analyses.
new_versions_of_features.pl  1.1  11 years  overbeek  add new_versions_of_features
nmpdr2gff.pl  1.1  11 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  11 years  overbeek  order_figfams
order_seqs_on_length.pl  1.1  10 years  overbeek  add utilities for computing alignments
order_sets.pl  1.3  12 years  olson  Add license words.
overlap_resolution_test.pl  1.2  3 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  1.1  15 months  parrello  Changes copied from SEEDtk project.
p3-aggregate-sss.pl  1.2  9 months  parrello  Changes copied from SEEDtk project.
p3-aggregates-to-html.pl  1.5  3 months  parrello  Changes copied from SEEDtk project.
p3-all-drugs.pl  1.4  4 months  parrello  Changes copied from SEEDtk project.
p3-all-genomes.pl  1.4  4 months  parrello  Changes copied from SEEDtk project.
p3-blast.pl  1.2  4 months  parrello  Changes copied from SEEDtk project.
p3-build-kmer-db.pl  1.1  4 months  parrello  Changes from SEEDtk.
p3-closest-seqs.pl  1.2  3 months  parrello  Changes copied from SEEDtk project.
p3-count.pl  1.1  3 months  parrello  Changes copied from SEEDtk project.
p3-drug-amr-data.pl  1.1  5 months  parrello  Changes copied from SEEDtk project.
p3-echo.pl  1.3  4 months  parrello  Changes from SEEDtk
p3-extract-gto.pl  1.5  5 months  parrello  Changes copied from SEEDtk project.
p3-extract.pl  1.5  4 months  parrello  Changes from SEEDtk
p3-feature-gap.pl  1.3  4 months  parrello  Changes copied from SEEDtk project.
p3-feature-upstream.pl  1.4  4 months  parrello  Changes copied from SEEDtk project.
p3-file-filter.pl  1.3  4 months  parrello  Changes copied from SEEDtk project.
p3-find-couples.pl  1.3  2 weeks  parrello  Updates from SEEDtk
p3-find-features.pl  1.1  3 months  parrello  Changes copied from SEEDtk project.
p3-find-in-clusters.pl  1.1  4 months  parrello  Changes from SEEDtk.
p3-format-results.pl  1.2  3 months  parrello  Changes copied from SEEDtk project.
p3-function-to-role.pl  1.3  4 months  parrello  Changes from SEEDtk
p3-generate-close-roles.pl  1.2  4 months  parrello  Changes from SEEDtk
p3-generate-clusters.pl  1.4  4 months  parrello  Changes copied from SEEDtk project.
p3-genome-amr-data.pl  1.2  5 months  parrello  Changes copied from SEEDtk project.
p3-genome-fasta.pl  1.4  3 months  parrello  Changes copied from SEEDtk project.
p3-genus-species.pl  1.1  3 months  parrello  Changes copied from SEEDtk project.
p3-get-contig-data.pl  1.2  5 months  parrello  Changes copied from SEEDtk project.
p3-get-drug-genomes.pl  1.4  4 months  parrello  Changes copied from SEEDtk project.
p3-get-family-data.pl  1.4  4 months  parrello  Changes copied from SEEDtk project.
p3-get-family-features.pl  1.4  4 months  parrello  Changes copied from SEEDtk project.
p3-get-feature-data.pl  1.6  2 weeks  olson  fix bug
p3-get-feature-group.pl  1.4  4 months  parrello  Changes copied from SEEDtk project.
p3-get-feature-sequence.pl  1.5  2 months  olson  Add metadata to the query_cb callback. Also use the return value of query_cb to ...
p3-get-features-by-sequence.pl  1.1  5 weeks  parrello  Changes copied from SEEDtk project.
p3-get-genome-contigs.pl  1.2  4 months  parrello  Changes from SEEDtk
p3-get-genome-data.pl  1.6  4 months  parrello  Changes copied from SEEDtk project.
p3-get-genome-drugs.pl  1.4  4 months  parrello  Changes copied from SEEDtk project.
p3-get-genome-features.pl  1.6  4 months  parrello  Changes copied from SEEDtk project.
p3-get-genome-group.pl  1.3  5 months  parrello  Changes copied from SEEDtk project.
p3-gto-dna.pl  1.1  3 months  parrello  Changes copied from SEEDtk project.
p3-gto-fasta.pl  1.1  4 months  parrello  Changes copied from SEEDtk project.
p3-gto-scan.pl  1.3  3 months  parrello  Changes copied from SEEDtk project.
p3-gto.pl  1.2  4 months  parrello  Changes from SEEDtk
p3-head.pl  1.1  4 months  parrello  Changes copied from SEEDtk project.
p3-identical-dna.pl  1.2  5 months  parrello  Changes copied from SEEDtk project.
p3-identical-proteins.pl  1.2  5 months  parrello  Changes copied from SEEDtk project.
p3-identify-clusters.pl  1.2  4 months  parrello  Changes copied from SEEDtk project.
p3-inAandB.pl  1.2  5 months  parrello  Changes copied from SEEDtk project.
p3-inAnotB.pl  1.2  5 months  parrello  Changes copied from SEEDtk project.
p3-inAorB.pl  1.2  5 months  parrello  Changes copied from SEEDtk project.
p3-join.pl  1.1  4 months  parrello  Changes from SEEDtk.
p3-kmer-compare.pl  1.1  3 months  parrello  Changes copied from SEEDtk project.
p3-list-feature-groups.pl  1.2  5 months  parrello  Changes copied from SEEDtk project.
p3-list-genome-groups.pl  1.2  5 months  parrello  Changes copied from SEEDtk project.
p3-login.pl  1.6  5 months  parrello  Changes copied from SEEDtk project.
p3-mass-cluster-run.pl  1.2  3 months  parrello  Changes copied from SEEDtk project.
p3-match.pl  1.6  4 months  parrello  Changes copied from SEEDtk project.
p3-merge.pl  1.1  5 weeks  parrello  Changes copied from SEEDtk project.
p3-pick.pl  1.1  15 months  parrello  Changes copied from SEEDtk project.
p3-project-subsystems.pl  1.1  5 months  parrello  Changes copied from SEEDtk project.
p3-put-feature-group.pl  1.4  5 months  parrello  Changes copied from SEEDtk project.
p3-put-genome-group.pl  1.4  5 months  parrello  Changes copied from SEEDtk project.
p3-rast.pl  1.3  4 months  parrello  Changes copied from SEEDtk project.
p3-related-by-clusters.pl  1.8  3 months  parrello  Changes copied from SEEDtk project.
p3-rep-prots.pl  1.1  4 months  parrello  Changes from SEEDtk.
p3-sequence-profile.pl  1.3  2 weeks  parrello  Updates from SEEDtk
p3-set-to-relation.pl  1.3  4 months  parrello  Changes copied from SEEDtk project.
p3-signature-clusters.pl  1.2  14 months  parrello  Changes copied from SEEDtk project.
p3-signature-families.pl  1.5  4 months  parrello  Changes from SEEDtk
p3-signature-peginfo.pl  1.2  4 months  parrello  Changes from SEEDtk
p3-similar-proteins-by-blast.pl  1.2  5 months  parrello  Changes copied from SEEDtk project.
p3-similar-proteins-by-family.pl  1.3  5 months  parrello  Changes copied from SEEDtk project.
p3-sort.pl  1.5  3 months  parrello  Changes copied from SEEDtk project.
p3-stats.pl  1.3  4 months  parrello  Changes from SEEDtk
p3-tbl-to-fasta.pl  1.1  4 months  parrello  Changes from SEEDtk.
p3-tbl-to-html.pl  1.1  2 weeks  parrello  Changes copied from SEEDtk project.
p3-tests.pl  1.2  4 months  parrello  Changes from SEEDtk.
p3_all_features.pl  1.1  2 years  olson  initial set of PATRIC data accessors. The p3* scripts have the same interface as...
p3_all_genomes.pl  1.1  2 years  olson  initial set of PATRIC data accessors. The p3* scripts have the same interface as...
p3_contigs_in_genome.pl  1.1  2 years  olson  initial set of PATRIC data accessors. The p3* scripts have the same interface as...
p3x-check-mcl-compute-times.pl  1.1  13 months  olson  P3 utility scripts.
p3x-compare-patric-calls-2.pl  1.1  13 months  olson  P3 utility scripts.
p3x-compare-patric-calls.pl  1.1  13 months  olson  P3 utility scripts.
p3x-compute-patric-update-delta.pl  1.1  2 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  2 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  2 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  13 months  olson  P3 utility scripts.
p3x-propagate-family-names.pl  1.1  13 months  olson  P3 utility scripts.
p3x-recall-patric-proteins.pl  1.1  13 months  olson  P3 utility scripts.
p3x-recall-proteins.pl  1.1  13 months  olson  P3 utility scripts.
p3x-reduce-families-for-kser.pl  1.1  13 months  olson  P3 utility scripts.
p3x-split-families.pl  1.1  13 months  olson  P3 utility scripts.
p3x-update-propagated-family-names.pl  1.1  13 months  olson  P3 utility scripts.
p3x-write-family-defs.pl  1.1  6 months  olson  Extract local and global family definition files from full family data.
p3x-write-subsystem-qa.pl  1.1  3 months  olson  New module for patric subsystem QA
p3x_kser_parallel_load.pl  1.1  2 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  1.2  2 weeks  parrello  Updates from SEEDtk
package_code.pl  1.2  12 years  olson  Add license words.
package_fix.pl  1.1  2 weeks  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  1.5  11 years  overbeek  fixes to deleted_features, replace_features_with, etc
package_translation_rules.pl  1.2  12 years  olson  Add license words.
paint_reactions_on_tree_pipeline.pl  1.2  4 years  overbeek  trying to commit a working copy
paint_tree.pl  1.3  12 years  olson  Add license words.
parse_genbank.pl  1.34  2 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  10 years  mkubal  v1
partition_prots.pl  1.5  4 years  overbeek  compute correspondences for a pan genome
patric_call_proteins.pl  1.4  18 months  olson  reduce fig obj creation
peg2pubmed.pl  1.1  11 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  8 years  overbeek  check for aux roles
pegs_in_subsystems.pl  1.8  8 years  overbeek  fix documentation
pegs_on_contigs.pl  1.2  11 months  parrello  Changes copied from SEEDtk project.
pg_add_genomes.pl  1.1  4 years  overbeek  add RAST genomeIDs to genome table
pg_add_role_peg.pl  1.4  4 years  overbeek  bad stuff
pg_adjacency_of_core.pl  1.2  4 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_build_fasta_for_phylogeny.pl  1.5  4 years  overbeek  updates induced by Bob
pg_build_newick_tree.pl  1.2  3 years  overbeek  use muscle for alignments
pg_build_protein_families.pl  1.4  4 years  overbeek  fixes to pan-genera pipeline
pg_check_gapfills.pl  1.1  4 years  overbeek  add gapfilling
pg_compute_corr.pl  1.3  4 years  overbeek  handle extraction of genome id better
pg_compute_md5s.pl  1.1  4 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_compute_subsystem_membership.pl  1.1  4 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_compute_traits.pl  1.3  4 years  overbeek  fix to pass2
pg_core_families.pl  1.8  4 years  overbeek  minor fix
pg_estimate_alien_pegs.pl  1.3  4 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_events.pl  1.2  4 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_extract_reaction_sets.pl  1.4  4 years  overbeek  fix eol
pg_filter_alien.pl  1.1  4 years  overbeek  reorder alien computation
pg_form_mobile_element_families.pl  1.3  4 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_function_of.pl  1.2  4 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_generate_possible_assignments.pl  1.1  4 years  overbeek  pg pipeline
pg_get_codon_usage_stats.pl  1.1  4 years  overbeek  add codon usage
pg_get_consistency_before_after.pl  1.2  4 years  overbeek  handle no assignments
pg_get_gapfill_reactions.pl  1.1  4 years  overbeek  add gapfilling
pg_get_models.pl  1.1  4 years  overbeek  add gapfilling
pg_get_pegs_in_repeats.pl  1.3  4 years  overbeek  set min overlap to 50
pg_get_reaction_keys.pl  1.1  4 years  overbeek  add gapfilling
pg_get_reaction_role.pl  1.1  4 years  overbeek  add gapfilling
pg_get_reactions.pl  1.1  4 years  overbeek  add gapfilling
pg_get_stats.pl  1.3  4 years  overbeek  fixes due to using nonRAST genomes
pg_inconsistent_families.pl  1.4  4 years  overbeek  strip comments
pg_intersection.pl  1.1  4 years  overbeek  add Jose stuff
pg_janaka_get_role_reactions_pegs.pl  1.4  4 years  overbeek  get rid of comments on functions
pg_make_initial_models.pl  1.12  4 years  overbeek  watch out for failing models
pg_make_md5_families.pl  1.5  4 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_make_reaction_properties.pl  1.1  4 years  overbeek  make reaction properties to paint tree
pg_make_reaction_tables.pl  1.1  4 years  overbeek  extract reaction table
pg_pipeline.pl  1.51  4 years  overbeek  readdble.tree is in Analysis
pg_process_pubs.pl  1.1  4 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_roles_in_some_but_not_X.pl  1.9  4 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_run_gapfills.pl  1.1  4 years  overbeek  add gapfilling
pg_submit_to_RAST.pl  1.3  4 years  overbeek  taxon id - not debugged
pg_tabulate_reactions.pl  1.2  4 years  overbeek  compute core reactions
pick_feature_set.pl  1.1  8 years  overbeek  choose genes from candidates
place_properties_on_tree.pl  1.6  2 years  overbeek  BAD BUG
place_proteins_into_pattyfams.pl  1.8  12 months  olson  Workaround for broken kser.
pop_vec.pl  1.2  4 years  overbeek  compute correspondences for a pan genome
possible_frameshifts.pl  1.1  10 years  overbeek  update possible_frameshifts
possible_projections.pl  1.1  5 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  11 years  overbeek  add potentially_missed_assignments
pp.pl  1.3  12 years  olson  Add license words.
predict_scenarios.pl  1.2  10 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  8 years  overbeek  basic metagenomic tools
prep_viz.pl  1.2  12 years  olson  Add license words.
prepare_metagenome_files_for_download.pl  1.4  9 years  mkubal  full loop
prepare_metagenome_files_for_ftp.pl  1.3  9 years  mkubal  checks for PUBLIC file
process_evaluation.pl  1.1  11 months  parrello  Changes copied from SEEDtk project.
process_genomes.pl  1.1  6 years  disz  Format new genomes for the Daily SEED
process_new_sims.pl  1.6  10 years  olson  Rollup of various rast-related changes.
process_one_exp_dir.pl  1.4  6 years  olson  fix typo
process_otus.pl  1.8  4 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  5 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  8 years  arodri7  commit changes
pubbed_fids.pl  1.1  8 years  parrello  New script to find features with publications attached.
publish_subsystems.pl  1.1  5 years  olson  script to programmagically publish a subsystem
pubmed_gene2peg.pl  1.2  11 years  redwards  making sure gene id is right
pubseed_data_export.pl  1.1  4 years  olson  Data exporter for pubseed.
pull_fasta_entries.pl  1.8  8 years  olson  do not attempt to remap incoming ids
pull_orfs.pl  1.8  23 months  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  11 years  overbeek  Removes duplicate entries from fasta file. -- /gdp
purge_tbl.pl  1.1  11 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  4 years  overbeek  get funcs
questionable_calls.pl  1.2  12 years  olson  Add license words.
rapid_propagation.pl  1.75  8 years  olson  use $num_neighbors internally instead of hardwired constant
rapid_propagation2.pl  1.5  7 years  gdpusch  Minor cosmetic changes.
rapid_propagation3.pl  1.10  7 years  olson  Support family determiantion.
rapid_propagation4.pl  1.11  11 months  gdpusch  Finally fixed (I hope!) the "Undefined Domain" bug.
rapid_propagation5.pl  1.2  23 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
rapid_propagation_plasmid.pl  1.22  7 years  disz  FigFam 6 digit problem
rapid_subsystem_inference.pl  1.22  2 years  overbeek  fix duplicate code
rapid_subsystem_inference_batch.pl  1.4  6 years  olson  Fix null-key bug
rast_annotate_proteins_similarity.pl  1.3  2 months  olson  Add -N option for annotate-null-only
rast_call_CDSs_using_prodigal.pl  1.6  2 years  olson  Propagate production fixes.
rast_call_RNAs.pl  1.3  2 years  olson  Propagate production fixes.
rast_call_crisprs.pl  1.4  2 years  olson  Propagate production fixes.
rast_call_prophage_using_phispy.pl  1.5  17 months  olson  Add non-failing diagnostic for input too small case.
rast_call_rRNAs.pl  1.8  23 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
rast_call_special_proteins.pl  1.12  2 months  olson  fix typo
rast_call_tRNAs.pl  1.5  2 years  olson  Propagate production fixes.
rast_compute_specialty_genes.pl  1.6  2 months  olson  Update to use blat and new thresholds.
rast_export_genome.pl  1.24  8 months  olson  For embl exports, truncate overlong taxonomy components.
rast_load_specialty_genes.pl  1.2  3 years  olson  Specialty protein & PATRIC caller code.
rast_prepare_NR_directory.pl  1.1  3 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  11 years  overbeek  RAE: Initial release of a simple script to read and write excel files to allow e...
readable_fasta.pl  1.1  5 years  overbeek  initial versions
rebuild_converged_Data.pl  1.7  16 months  olson  Commit updates to kmer build code.
rebuild_global_chromosomal_clusters.pl  1.2  10 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  5 years  disz  create data for the Daily SEED
recompute_comparison.pl  1.1  9 years  bartels  *** empty log message ***
reduce_sims.pl  1.12  8 years  olson  fix nasty little bug that drops sims
reformat_circular_contigs.pl  1.1  8 years  arodri7  added reformat_circular_contigs for rapid_propagation_plasmids
reformat_contigs.pl  1.26  9 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  10 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
reformat_timelogic_sims.pl  1.2  10 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  10 years  olson  Missing scripts.
reindex_sim_btrees.pl  1.1  5 years  olson  new script to update btree indexes of sims files in a genome dir
rel2tabs.pl  1.3  2 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  10 years  olson  Missing scripts.
remove_clustered_pchs3.pl  1.1  10 years  olson  Missing scripts.
remove_embedded_pegs.pl  1.19  7 years  gdpusch  Modified to use Kmers.
remove_multiple_occurring_probes.pl  1.2  6 years  olson  exp fixes
remove_rna_overlaps.pl  1.11  23 months  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  10 years  olson  Missing scripts.
renumber_features.pl  1.14  23 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
renumber_seed_dir.pl  1.8  9 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  8 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  10 years  overbeek  add make_trimmed_alignment_from_ids
reps_for_wc.pl  1.2  2 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  4 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  3 years  overbeek  root a tree at the midpoint
rs.pl  1.2  3 years  overbeek  compute mean/stddev of positive hits
rs_create_ref_profile.pl  1.1  4 years  overbeek  the rna_seq pipeline
rs_get_intergenic_counts.pl  1.1  4 years  overbeek  the rna_seq pipeline
rs_get_peg_counts.pl  1.1  4 years  overbeek  the rna_seq pipeline
rs_get_rnas.pl  1.1  4 years  overbeek  the rna_seq pipeline
rs_pipeline.pl  1.1  4 years  overbeek  the rna_seq pipeline
run1_convergence_step.pl  1.7  16 months  olson  Commit updates to kmer build code.
run_HMM_search_on_timelogic.pl  1.1  10 years  mkubal  version 1.0
run_all_fam_rel.pl  1.1  15 months  parrello  Changes copied from SEEDtk project.
run_all_inference.pl  1.2  6 years  olson  Run on all genomes; update anything either missing a subsystems file or that hav...
run_anno_to_pubseed_flow.sh  1.6  4 years  olson  fix missing \
run_checkm.pl  1.1  13 months  parrello  Changes copied from SEEDtk project.
run_coreseed_to_pubseed_flow.sh  1.1  4 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  10 years  overbeek  updates to computation of VCs
run_flux_optimization.pl  1.4  9 years  dejongh  switch to scenario_directory
run_gene_calling_scripts.pl  1.3  8 years  overbeek  fix first arg on call to mark_picked_genes
run_glimmer2.pl  1.7  10 years  gdpusch  Added support for multiple genetic codes. -- /gdp
run_glimmer3.pl  1.14  7 years  parrello  Added "-verbose" option so tracing can be turned on from the servers.
run_model_generation.pl  1.17  9 years  dejongh  switch to scenario_directory
run_model_generation_all.pl  1.1  10 years  formsma  This script will generate models for all complete genomes in the seed. - Kevin
run_model_generation_v3.pl  1.3  9 years  dejongh  switch to scenario_directory
run_muscle.pl  1.3  6 years  golsen  Update libraries used.
run_peg_job_worker.pl  1.4  12 years  olson  Add license words.
run_rabbit_daemon.pl  1.5  5 years  olson  Add memcached support
run_rabbit_daemon_set.pl  1.3  6 years  olson  remove debug
run_remote_PHOBIOUS.pl  1.1  10 years  mkubal  runs Phobius computation for given geneome
run_remote_Phobius_for_fasta.pl  1.1  9 years  mkubal  fasta file as input
run_remote_Phobius_for_genome.pl  1.1  10 years  mkubal  for single genome
run_remote_Phobius_for_genome_for_RAST.pl  1.1  10 years  mkubal  for use with RAST server
run_remote_Phobius_for_genomes.pl  1.1  10 years  mkubal  run for all complete prok genomes
run_ribo_ratio_against_pubseed.pl  1.1  4 years  overbeek  quality control using ribo proteins
run_scenarios.pl  1.5  9 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  10 years  overbeek  add computation of alignments to building FIGFAMS
salvage_annotations.pl  1.6  11 years  olson  bugfix.
salvage_master_annotations.pl  1.3  11 years  overbeek  fixes to salvage code
salvage_subsystem_rows.pl  1.6  11 years  overbeek  fixes to salvage code
same_figfam.pl  1.2  10 years  overbeek  handle bad input in same_figfam
same_subsys.pl  1.1  11 years  overbeek  fixes to extract_genomes
score_dfcs.pl  1.3  11 years  overbeek  RAE: removing the header that should not be in the source
score_dfcs_mcauliffe.pl  1.5  11 years  overbeek  limit decimal positions in score
score_ifcs.pl  1.4  11 years  overbeek  RAE: More direct and indirect functional coupling scores
score_ifcs_mcauliffe.pl  1.2  11 years  overbeek  RAE: correcting indirect functional coupling score
seed2genbank.pl  1.6  5 years  redwards  adding SOURCE and taxonomy information
seed2gff.pl  1.36  9 years  redwards  getting rid of need for strain info
seed2pir.pl  1.3  11 years  overbeek  RAE: moving PIRSF to links
seed2ptt.pl  1.2  4 years  redwards  adding alternate genome selections
seed2tbl.pl  1.3  7 years  disz  FigFam 6 digit problem
seed2txt.pl  1.1  6 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  11 years  olson  readonly fixes; seed-run-job update to run from input file
seed_run_task.pl  1.2  11 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  8 years  arodri7  first version of sequence_dereplication. Script takes sequences which are subset...
sequence_length_histogram.pl  1.6  7 years  olson  Include in SAS
server_paper_example1.pl  1.12  7 years  parrello  Documentation fix for server paper.
server_paper_example2.pl  1.7  7 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  7 years  parrello  Fixed to use the correct servers.
server_paper_example5.pl  1.3  7 years  disz  Switched to ANNO server
server_paper_example6.pl  1.3  7 years  parrello  Fixed for server paper.
server_paper_example7.pl  1.4  7 years  chenry  Corrected a few bugs in the example script.
server_paper_figure2.pl  1.2  7 years  parrello  Removed genetic codes so program fits better on a page.
set-from-subtree.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
set_by_subtree.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
set_figfam_functions.pl  1.1  5 years  overbeek  to support assigning FigFam functions
set_not_private.pl  1.1  9 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  9 years  disz  Ross's code to generate annotations for NCBI
sigs.pl  1.2  5 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  4 years  redwards   a set of scripts for adding phage genomes to the seed
sims_all.pl  1.6  8 years  overbeek  remove paralogs before computing conections
sims_between.pl  1.7  10 years  overbeek  updates on close connections
sketch_tree.pl  1.5  4 years  olson  Revive this script.
solid_rectangles_to_solid_families.pl  1.1  4 years  overbeek  format output
sort_and_split_bbhs.pl  1.5  10 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
sort_by_annotator.pl  1.2  6 years  disz  Fixed bad links
sort_by_function.pl  1.2  6 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  4 years  golsen  A script to provide a set of diverse genomes (< 90% identical) that are similar ...
sphinx_index_genome.pl  1.14  22 months  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  10 years  overbeek  fix problem when repeats occur
split_assignments_based_on_subsystems.pl  1.1  11 years  overbeek  next version of the STAG code
split_by_genome.pl  1.1  11 years  overbeek  split_by_genome can be used to split a score or BBH file
split_clean_unclean_families.pl  1.4  11 years  overbeek  fixes for splitting families into clean/unclean
split_fasta.pl  1.1  2 years  olson  Script to split a fasta file into chunks of a given size.
split_sequences_into_sets.pl  1.5  8 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  4 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  2 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  5 years  overbeek  create new saved correspondences
submit_corr_to_server.pl  1.2  5 years  overbeek  fefault value for map submission
submit_ff_test.pl  1.6  8 years  arodri7  commit changes
submit_genome_to_rpsblast_against_CDD_on_biocluster.pl  1.2  10 years  mkubal  test for dir exist
submit_genome_to_signalP.pl  1.2  10 years  mkubal  test for dir exist
submit_to_iprscan_on_biocluster.pl  1.1  10 years  mkubal  run iprscan on cluster
subsys2pubmed.pl  1.4  10 years  hwang  change script to add new attribute after each subsystem versus after all subsyst...
subsys_info.pl  1.1  9 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  4 years  overbeek  summarize classification output
summarize_genome_data.pl  1.1  4 years  overbeek  create summary_of_genome data
summarize_taxonomy_by_blast.pl  1.9  9 years  redwards  removing fatal error if 0 or 1 hits
svc_fasta_to_md5.pl  1.2  20 months  parrello  Changes copied from SEEDtk project.
svr.pl  1.2  7 years  olson  add . to include path
svr_ACH.t  1.1  8 years  olson  new tests
svr_CS.pl  1.8  4 weeks  olson  Add support for pulling genomes from PATRIC
svr_CS_pipeline.pl  1.6  3 years  overbeek  compute adjacency data for What Changed?
svr_NCBI_sequence.pl  1.1  2 years  golsen  A script for retrieving sequence and related data from NCBI. Output can be tab d...
svr_NCBI_taxonomy.pl  1.2  6 years  golsen  Add more formats in which abbreviated lineages can be returned. Add long form of...
svr_RNA_genes.pl  1.6  2 years  golsen  Improve comments.
svr_SAP.t  1.4  7 years  olson  update tests
svr_ach_lookup.pl  1.10  7 years  parrello  More server script stuff. Thought I'd already installed these last week...
svr_add_lengths_to_blast.pl  1.1  6 years  overbeek   simple utility to add sequence lengths to m8 blast output
svr_add_reaction_descriptions.pl  1.1  4 years  overbeek  a tool to add reaction descriptions
svr_ali_to_html.pl  1.4  5 years  fangfang  fixed bug for the no color option by using Gary's new repad_alignment code
svr_aliases_of.pl  1.7  6 years  parrello  Fixed for better flow control.
svr_aliases_to_pegs.pl  1.1  7 years  parrello  New script for Ross
svr_align_seqs.pl  1.15  5 years  overbeek  allow option to preserve sequence order
svr_align_using_muscle.pl  1.2  7 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  6 years  parrello  Added to get experiments for each genome.
svr_all_features.pl  1.7  6 years  olson  Deobfuscate the command line logic. Submit requests in chunks so as to not be pa...
svr_all_figfams.pl  1.2  7 years  parrello  Documentation fixes.
svr_all_genomes.pl  1.3  6 years  overbeek  support restriction to proks
svr_all_models.pl  1.2  6 years  overbeek  keep only Seed models
svr_all_reactions.pl  1.1  6 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  7 years  parrello  Fixed POD errors. Added examples.
svr_assign_to_dna_using_figfams.pl  1.18  5 years  olson  add prot length and genus
svr_assign_using_figfams.pl  1.13  3 years  overbeek  describe output more accurately
svr_atomic_reg_coexp.pl  1.1  5 years  overbeek  initial version
svr_atomic_regulons.pl  1.1  6 years  parrello  Added to allow retrieval of pegs in atomic regulons.
svr_big_repeats.pl  1.3  3 years  olson  add error message to failure messages
svr_blast.pl  1.2  3 years  overbeek  compute mean/stddev of positive hits
svr_by_taxonomy.pl  1.3  7 years  overbeek  fix parameter passing
svr_call_pegs.pl  1.2  7 years  overbeek  fix POD stuff
svr_call_rnas.pl  1.2  6 years  overbeek  fix pod doc
svr_cdd_scan.pl  1.3  6 years  fangfang  retrieve non-specific hits for full mode
svr_close_genomes.pl  1.2  4 years  overbeek  compute correspondences for a pan genome
svr_closest_genes.pl  1.1  7 years  parrello  More server script stuff.
svr_cluster_locations.pl  1.1  3 years  overbeek  compute clusters
svr_cluster_pegs.pl  1.1  7 years  overbeek  two small utilities
svr_co_occurrence_evidence.pl  1.4  7 years  disz  FigFam 6 digit problem
svr_cohesion_groups.pl  1.4  6 years  fangfang  update
svr_column_of_subsystem.pl  1.1  7 years  olson  server script to pull a subsystem colum
svr_compare_feature_tables.pl  1.7  7 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  3 years  overbeek  throw out overlapping
svr_contigs_in_genome.pl  1.3  7 years  parrello  Added support for specifying input IDs on the command line.
svr_copy_to_RAST_dir.pl  1.3  7 years  olson  fix
svr_coregulated_by_correspondence.pl  1.7  4 years  overbeek  compute correspondences for a pan genome
svr_corr_by_exp.pl  1.5  6 years  parrello  Changed to batch the input instead of slurping it.
svr_corresponding_genes.pl  1.24  7 years  overbeek  fix command line arguments
svr_corresponding_genes2.pl  1.7  22 months  olson  Revert to 1.5.
svr_coupled_reactions.pl  1.1  6 years  parrello  New chemistry-based scripts.
svr_create_set.pl  1.1  6 years  disz  New persistent set svr scripts
svr_current_annotation.pl  1.4  5 years  fangfang  fix bug
svr_cut_domain.pl  1.1  7 years  overbeek  cut domains from sequences
svr_delete_RAST_job.pl  1.3  8 years  olson  Fix 666666 problem. Add support for using the test server.
svr_delete_from_set.pl  1.1  6 years  disz  New persistent set svr scripts
svr_delete_set.pl  1.1  6 years  disz  New persistent set svr scripts
svr_determine_sets_of_related_contigs.pl  1.4  7 years  parrello  Documentation fixes.
svr_discriminating_functions.pl  1.3  7 years  parrello  Discrimination functions support scripts.
svr_distinct_otus.pl  1.4  7 years  parrello  Added support for specifying input IDs on the command line.
svr_dlits.pl  1.1  6 years  parrello  New script to call dlits_for_ids
svr_dna_seq.pl  1.2  7 years  parrello  More server script stuff.
svr_drug_resistance_proteins.pl  1.3  3 years  fangfang  fix merge conflict
svr_enumerate_sets_by_owner.pl  1.1  6 years  disz  New persistent set svr scripts
svr_evidence.pl  1.1  7 years  disz  New svr script to get evidence code
svr_exp_genomes.pl  1.1  6 years  parrello  New script to list expression-data genomes.
svr_export_as_seed_dir.pl  1.3  6 years  olson  bugfix, get all subsystem records.
svr_expressed_genes_in_range.pl  1.1  6 years  parrello  Added for looking at genes that are never or always expressed.
svr_fasta.pl  1.14  6 years  overbeek  wrap the seq into 60-char lines
svr_fasta_to_md5.pl  1.1  6 years  parrello  New script for computing MD5s from FASTA protein sequences.
svr_fc_figfams.pl  1.3  7 years  overbeek  sort by score
svr_fids_for_md5.pl  1.1  6 years  parrello  New method to return FIG IDs for a protein given its MD5.
svr_fids_to_ids.pl  1.1  4 years  gdpusch  Initial checkin of script to fetch external ("alias") IDs for a FID.
svr_fids_to_locations.pl  1.1  3 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  7 years  parrello  More server script stuff. Thought I'd already installed these last week...
svr_figfam_functions.pl  1.2  7 years  parrello  Added option to get all the FIGfams.
svr_figfams_to_ids.pl  1.6  7 years  parrello  Added "roles_to_subsys", sped up "figfams_to_ids", fixed pod for "mapped_genomes...
svr_file_to_spreadsheet.pl  1.3  6 years  olson  If -u url flag is added, add links to pegs.
svr_find_clusters_relevant_to_reaction.pl  1.6  4 years  overbeek  compute correspondences for a pan genome
svr_find_fused_genes.pl  1.3  6 years  fangfang  updated POD
svr_find_hypos_for_cluster.pl  1.1  6 years  overbeek  find hypotheticals associated with clusters
svr_find_protein.pl  1.2  6 years  parrello  Fixed the error reporting.
svr_find_regulatory_proteins.pl  1.1  7 years  overbeek  a simple tool to find potential regulatory proteins
svr_function_of.pl  1.15  3 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  6 years  overbeek  add cutoffs
svr_gap_filled_reactions_and_roles.pl  1.5  6 years  devoid  fixing some problems with authentication, error reporting
svr_genbank_to_seed.pl  1.4  9 months  gdpusch  Extract RNAs as well as PEGs.
svr_genbank_to_table.pl  1.2  7 years  gdpusch  Added various alias IDs to output.
svr_gene_data.pl  1.3  7 years  parrello  First round of script updates & additions for tutorial.
svr_generate_dna_samples.pl  1.1  4 years  overbeek  basic kmer validation tools
svr_genome_functions.pl  1.3  7 years  overbeek  sort by feature id
svr_genome_of.pl  1.1  6 years  overbeek  genome of feature
svr_genome_statistics.pl  1.2  7 years  parrello  Added genome name to the POD.
svr_get_ali_and_tree.pl  1.1  6 years  overbeek  get alignment and tree from seq(s)
svr_get_all.pl  1.2  4 years  olson  Make array-valued fields be returned as comma-joined.
svr_get_coupling_data.pl  1.2  6 years  overbeek  must have -d
svr_get_default_dataset.pl  1.1  6 years  olson  script to retrieve the name of the current default kmer datasets
svr_get_rep_genomes.pl  1.2  4 years  overbeek  minor fix of documentation
svr_get_set.pl  1.2  6 years  disz  New persistent set svr scripts
svr_identical_genomes.pl  1.2  5 years  overbeek  return seed, as well
svr_ids_to_figfams.pl  1.8  7 years  overbeek  fixes to documentation
svr_ids_to_subsystems.pl  1.6  7 years  disz  Added stderr output for non-matches
svr_img_analysis.pl  1.5  5 years  parrello  Converted to new interface.
svr_in_fasta.pl  1.1  4 years  overbeek  compute correspondences for a pan genome
svr_in_runs.pl  1.5  7 years  parrello  Fixed POD errors. Added examples.
svr_inconsistent_sets.pl  1.5  6 years  overbeek  minor fixes
svr_inherit_aliases.pl  1.5  6 years  gdpusch  Fixed mapping failure.
svr_inherit_annotations.pl  1.3  6 years  gdpusch  Saved ouput of ID mapping to file "inheritance.id_map," and added some bulletpro...
svr_insert_seqs_into_alignment.pl  1.2  7 years  fangfang  take advantage of gjoseqlib's flexible API to implicitly interact with STDIN/STD...
svr_intergenic_regions.pl  1.1  7 years  parrello  New script to find intergenic regions.
svr_is_hypo.pl  1.3  6 years  overbeek  minor fixes
svr_just_ends.pl  1.3  6 years  redwards  increasing min length to 2000 so that you have two ends!
svr_keep_only.pl  1.1  7 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  6 years  fangfang  fixed typo in $genomeH
svr_location_of.pl  1.2  3 years  parrello  CDMI and Sprout load fixes. Locations fixes.
svr_make_pan_genome_prot_families.pl  1.10  5 years  overbeek  fix bad comments
svr_mapped_genomes.pl  1.4  6 years  parrello  Fixed a leftover hack.
svr_mark_tree_states.pl  1.5  4 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  4 years  overbeek  add entry for rep
svr_metabolic_reconstruction.pl  1.5  7 years  olson  bah, fix paste error
svr_missing_roles.pl  1.2  6 years  overbeek  added -g genome
svr_motif.pl  1.4  6 years  fangfang  simplify code
svr_neighborhood_of_role.pl  1.3  6 years  parrello  Converted to use chemistry data instead of the models.
svr_neighboring_reactions.pl  1.2  6 years  overbeek  minor fixes
svr_neighbors_of.pl  1.5  3 years  overbeek  error checking
svr_oligomer_similarity.pl  1.1  7 years  overbeek  compute oligo similarities
svr_otus.pl  1.3  7 years  overbeek  minor fixes
svr_pegs_in_subsystems.pl  1.7  6 years  parrello  Fixed to process 10 subsystems at a time, reducing the chances of a timeout.
svr_pegs_with_evcode.pl  1.2  6 years  overbeek  must have genomes specified
svr_possible_joins.pl  1.1  7 years  overbeek  tools to try to bridge contigs
svr_preferred_roles.pl  1.6  2 years  overbeek  translation fixes
svr_project_by_sr.pl  1.1  4 years  overbeek  project with SRs
svr_project_model.pl  1.2  5 years  overbeek  effectors are not required input
svr_protein_assertions.pl  1.6  7 years  disz  CHanged ACHserver to SAPserver and fixed processing of return values
svr_psiblast_search.pl  1.28  3 years  fangfang  add core seed db
svr_put_set.pl  1.1  6 years  disz  New persistent set svr scripts
svr_quick_assign.pl  1.3  3 years  olson  Add tempdir()/tempfile() calls to manage create temps in right place. Add status...
svr_rRNA.pl  1.2  6 years  fangfang  update pod
svr_reaction_description.pl  1.3  6 years  parrello  Added -f flag.
svr_reaction_gain_loss_table.pl  1.1  4 years  golsen  Tools for mapping reaction presence and absence onto a tree.
svr_reactions_in_model.pl  1.1  6 years  parrello  New script for Ross.
svr_reactions_to_roles.pl  1.1  6 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  3 years  fangfang  add -a n_thread option
svr_reroot_tree.pl  1.3  7 years  overbeek  fix typo
svr_retrieve_RAST_job.pl  1.3  8 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  6 years  overbeek  mispelled genome with bad consequences
svr_roles_to_reactions.pl  1.2  4 years  overbeek  get reactions implied by roles
svr_roles_to_subsys.pl  1.3  2 years  redwards  changing the separator in SS classifcations
svr_run_RAST_jobs.pl  1.7  6 years  olson  Add kmerDataset selection support.
svr_scanN.pl  1.1  6 years  overbeek  scanning utilities
svr_scanP.pl  1.2  6 years  overbeek  add a little documentation
svr_scripts.t  1.2  8 years  olson  updated tests
svr_seed_to_embl.pl  1.2  23 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
svr_seed_to_genbank.pl  1.3  23 months  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  6 years  disz  enumerate sets by owner
svr_similar_to.pl  1.2  7 years  parrello  Fixed POD errors.
svr_sims2html.pl  1.6  7 years  golsen  Add pod documentation.
svr_sketch_tree.pl  1.4  6 years  golsen  Trivial change to the usage information.
svr_sphinx_indexing.pl  1.1  3 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  6 years  disz  Fixed missing file error message
svr_ss_classes.pl  1.1  6 years  parrello  Added to get classification data for subsystems.
svr_status_of_RAST_job.pl  1.4  7 years  olson  add url argument
svr_submit_RAST_job.pl  1.17  18 months  olson  Add rasttk submission support
svr_submit_correspondences.pl  1.2  6 years  parrello  Enhanced to handle Ross's alternate directory structure for correspondence maps....
svr_subsystem_classification.pl  1.1  6 years  gdpusch  Initial prototype checkin, still missing bells and whistles.
svr_subsystem_genome_data.pl  1.1  7 years  parrello  More server scripts.
svr_subsystem_genomes.pl  1.1  7 years  parrello  Discrimination functions support scripts.
svr_subsystem_roles.pl  1.2  6 years  overbeek  allow ss from stdin
svr_subsystem_spreadsheet.pl  1.1  7 years  parrello  subsystem download scripts.
svr_subsystems_to_roles.pl  1.1  3 years  overbeek  get roles of subsystems
svr_summarize_MG_output.pl  1.4  7 years  overbeek  extend the number of digits in the fraction of the total
svr_summarize_contigs.pl  1.2  7 years  parrello  New script, some documentation fixes.
svr_summarize_protein_families.pl  1.2  7 years  overbeek  minor changes
svr_tab2html.pl  1.5  7 years  gdpusch  Fixed a bug I introduced, and added a "--border" option to the table.
svr_taxonomically_related_genomes.pl  1.10  6 years  fangfang  update POD
svr_taxonomy.pl  1.4  5 years  fangfang  Added flag for taxonomy level
svr_tips_of_tree.pl  1.2  7 years  overbeek  add correspondence translation
svr_tmpred_predictions.pl  1.2  5 years  overbeek  fix_comment
svr_translations_of.pl  1.6  6 years  golsen  Add an option of genome names in the output. Clean up the way functions are adde...
svr_tree.pl  1.10  6 years  fangfang  add parallel support for bootstrap
svr_tree_to_html.pl  1.14  2 years  fangfang  add fetch_seed_gto.pl
svr_trim_ali.pl  1.10  6 years  fangfang  fix description field in trim html
svr_update_assignments.pl  1.3  7 years  gdpusch  Fixed typo.
svr_update_corr_maps.pl  1.2  6 years  overbeek  minor fix
svr_upstream.pl  1.9  3 years  parrello  CDMI and Sprout load fixes. Locations fixes.
svr_which_genus_species.pl  1.1  4 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  2 years  parrello  Changes copied from SEEDtk project.
test_Observation.pl  1.1  10 years  mkubal  for testing
test_cv.expected  1.1  12 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  9 years  olson  Missed one of the figfamdata fixes.
test_figfam_peg.pl  1.6  9 years  arodri7  update changes
test_figfam_placement_into_families.pl  1.10  7 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  10 years  overbeek  redone FIGfam stuff
tips_of.pl  1.3  10 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  10 years  hwang  This script parses arabidopsis.org to get the AT aliases output
to_fasta.pl  1.1  5 years  overbeek  initial versions
to_genbank.pl  1.7  7 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  11 years  hwang  fix syntax error
to_prodom.pl  1.7  8 years  olson  fix updated URL
to_run_daily.sh  1.4  5 years  disz  Updated to use recent_annotations_by_genome
to_run_new_genomes.sh  1.3  6 years  disz  Added source of environment
to_structured_english.pl  1.1  9 years  overbeek  add routine to build structured english rendering of evidence codes
trace.pl  1.3  9 years  parrello  Fixed so that the destination is not case-sensitive.
track_figfams.pl  1.2  11 years  overbeek  get rid of diagnostics in track_figfams
trail.pl  1.1  5 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  5 years  golsen  Support for codon usage analyses.
translate_fasta_6.c  1.2  2 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  10 years  overbeek  minor fixes
trim_sequences.pl  1.11  8 years  overbeek  fixes bug in handling multidomain prots
trimmed_kernel_alignment.pl  1.1  10 years  overbeek  add last round of phylogeny tools
uni_lit_to_dlits.pl  1.1  9 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  10 years  olson  Update SEED caches.
update_FIGfams.pl  1.12  8 years  arodri7  commit changes
update_OTUs.pl  1.5  6 years  overbeek  fix OTU update to use gary olsen sequence grouping script
update_PSEED_subsystems.pl  1.3  7 years  olson  add doc
update_SSU_rRNAs.pl  1.1  8 years  overbeek  update of SSUs
update_fr2go.pl  1.1  11 years  overbeek  put in the fr2go stuff
update_hope_info.pl  1.4  7 years  dejongh  added comments
update_kegg_data.pl  1.6  7 years  dejongh  removed comment
update_lineage.pl  1.3  9 years  wilke  draft version to update FIG taxonomy entries
update_nr_cycle.pl  1.6  11 years  overbeek  load ext org table on update_nr_cycle
update_phage_annotations.pl  1.1  4 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  7 years  olson  updated code
update_taxonomies.pl  1.9  11 months  olson  Revamp of this script to use efetch utility instead of parsing webpage and to ta...
update_uniq_id_data.pl  1.7  10 years  olson  use function_of_quick
uproot.pl  1.1  10 years  overbeek  add uproot
upstream.pl  1.3  12 years  olson  Add license words.
valid_fasta_file.pl  1.1  7 years  olson  Check to ensure a fasta file is valid.
validate_fasta.pl  1.1  10 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  1.42  6 years  gdpusch  Added recognition of "contig.properties" file.
verify_pegs_in_tbl.pl  1.2  12 years  olson  Add license words.
wb.pl  1.1  7 years  overbeek  workbench for alignments and trees
weak_predictors.pl  1.1  3 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  4 years  overbeek  fix child check
write_go_mappings.pl  1.4  3 years  olson  Specialty protein & PATRIC caller code.

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