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File Rev. Age Author Last log entry
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svr_big_repeats.pl  1.4  4 days  olson  Remove hard dependency on full SEED environment.
svr_condense_repeats.pl  1.4  4 days  olson  Remove hard dependency on full SEED environment.
reformat_contigs.pl  1.27  4 weeks  gdpusch  Major rewrite, processing sequences using 'gjoseqlib' and arguments using 'Getop...
find_approx_neigh.pl  1.9  8 weeks  gdpusch  Added some code to ensure that this tool only returns genomes that are installed...
rast_delete_rejected_pegs.pl  1.1  2 months  gdpusch  Script to delete PEGs that were rejected during final verification
place_proteins_into_pattyfams.pl  1.9  2 months  olson  Do not emit calls if score is zero. Annotate GTO output with score.
p3-genome-kmer-hits.pl  1.2  6 months  parrello  Updates from SEEDtk
rast_export_genome.pl  1.26  7 months  olson  Add pgfam/plfam to export
find_IS.pl  1.9  7 months  olson  Change default blastx parallelism from 12 to 2 (consumes lots of system CPU in t...
p3-discriminating-kmers.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3-role-features.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3-signature-families.pl  1.7  7 months  parrello  Changes copied from SEEDtk project.
p3-write-kmers.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3-get-genome-subsystems.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3x-eval-bins.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-genome-distance.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3-join.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-get-feature-regions.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3-get-feature-subsystems.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3-gto.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-subsys-roles.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3x-eval-genomes.pl  1.3  7 months  parrello  Changes copied from SEEDtk project.
p3-uni-roles.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3-tail.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3-match.pl  1.7  7 months  parrello  Changes copied from SEEDtk project.
p3-function-parse.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3-all-subsystems.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3x-test-evaluator.pl  1.2  7 months  parrello  Changes copied from SEEDtk project.
p3-merge.pl  1.2  7 months  parrello  Changes copied from SEEDtk project.
p3-stats.pl  1.5  7 months  parrello  Changes copied from SEEDtk project.
p3-rep-prots.pl  1.5  7 months  parrello  Changes copied from SEEDtk project.
p3-feature-upstream.pl  1.6  7 months  parrello  Changes copied from SEEDtk project.
plate_sheet_parser.pl  1.2  7 months  parrello  Changes copied from SEEDtk project.
p3-all-taxonomies.pl  1.1  7 months  parrello  Changes copied from SEEDtk project.
p3-find-couples.pl  1.7  7 months  parrello  Changes copied from SEEDtk project.
p3-sort.pl  1.8  7 months  parrello  Changes copied from SEEDtk project.
gto_to_tbl.pl  1.3  7 months  gdpusch  Fixed missing comma in arguments to &SeedUtils::min()
p3-get-genome-features.pl  1.10  12 months  parrello  Changes copied from SEEDtk project.
p3-get-feature-data.pl  1.10  12 months  parrello  Changes copied from SEEDtk project.
p3-get-genome-expression.pl  1.3  12 months  parrello  Changes copied from SEEDtk project.
p3-get-drug-genomes.pl  1.7  12 months  parrello  Changes copied from SEEDtk project.
p3-get-genome-contigs.pl  1.5  12 months  parrello  Changes copied from SEEDtk project.
p3-get-genome-data.pl  1.10  12 months  parrello  Changes copied from SEEDtk project.
p3-get-genome-drugs.pl  1.8  12 months  parrello  Changes copied from SEEDtk project.
dose_response_sheets.pl  1.2  12 months  parrello  Changes copied from SEEDtk project.
eval_matrix.py  1.2  12 months  parrello  Changes copied from SEEDtk project.
dose_response_extract.pl  1.2  12 months  parrello  Changes copied from SEEDtk project.
p3-get-family-data.pl  1.6  12 months  parrello  Changes copied from SEEDtk project.
p3x-eval-gto.pl  1.1  12 months  parrello  Changes copied from SEEDtk project.
p3-co-occur.pl  1.2  12 months  parrello  Changes copied from SEEDtk project.
p3x-eval-bin-site.pl  1.2  12 months  parrello  Changes copied from SEEDtk project.
ic50_compare.pl  1.1  12 months  parrello  Changes copied from SEEDtk project.
p3-get-family-features.pl  1.7  12 months  parrello  Changes copied from SEEDtk project.
p3-all-drugs.pl  1.7  12 months  parrello  Changes copied from SEEDtk project.
collate_reads.pl  1.1  12 months  parrello  Changes copied from SEEDtk project.
p3-tests.pl  1.5  12 months  parrello  Changes copied from SEEDtk project.
dose_response_ic50.pl  1.2  12 months  parrello  Changes copied from SEEDtk project.
p3-all-genomes.pl  1.8  12 months  parrello  Changes copied from SEEDtk project.
build_sample_sigs.pl  1.1  12 months  parrello  Changes copied from SEEDtk project.
p3-find-features.pl  1.4  12 months  parrello  Changes copied from SEEDtk project.
build_family_dir_from_genera.pl  1.3  12 months  olson  Checkpoint before viruses change.
rast_call_crisprs.pl  1.6  13 months  olson  Don't require KB IDServer
rast_annotate_proteins_similarity.pl  1.4  13 months  olson   Don't require KB IDserver
rast_call_prophage_using_phispy.pl  1.6  13 months  olson  Modifications for compiling without KB IDServer module. Add assembly gap caller....
rast_call_special_proteins.pl  1.13  13 months  olson  Modifications for compiling without KB IDServer module. Add assembly gap caller....
rast_call_CDSs_using_prodigal.pl  1.7  13 months  olson  Modifications for compiling without KB IDServer module. Add assembly gap caller....
rast_call_assembly_gaps.pl  1.1  13 months  olson  Modifications for compiling without KB IDServer module. Add assembly gap caller....
rast_call_tRNAs.pl  1.6  13 months  olson  Modifications for compiling without KB IDServer module. Add assembly gap caller....
rast_call_rRNAs.pl  1.9  13 months  olson  Don't require KB idserver
rast_build_nr_from_close_genomes.pl  1.1  13 months  gdpusch  Initial checkin. Script to build and formatdb a local NR in a RAST directory fro...
package_cleaned_bins.pl  1.3  14 months  parrello  Changes copied from SEEDtk project.
p3-echo.pl  1.4  14 months  parrello  Changes copied from SEEDtk project.
cluster_objects.pl  1.10  14 months  parrello  Changes copied from SEEDtk project.
p3x-eval-genome.pl  1.1  14 months  parrello  Changes copied from SEEDtk project.
p3-get-feature-group.pl  1.6  14 months  parrello  Changes copied from SEEDtk project.
p3-role-matrix.pl  1.2  14 months  parrello  Changes copied from SEEDtk project.
p3-put-feature-group.pl  1.5  14 months  parrello  Changes copied from SEEDtk project.
cripple_gto.pl  1.2  14 months  parrello  Changes copied from SEEDtk project.
p3-collate.pl  1.1  14 months  parrello  Changes copied from SEEDtk project.
check_gto.pl  1.1  14 months  parrello  Changes copied from SEEDtk project.
p3-put-genome-group.pl  1.5  14 months  parrello  Changes copied from SEEDtk project.
p3-extract.pl  1.6  14 months  parrello  Changes copied from SEEDtk project.
p3-file-filter.pl  1.5  14 months  parrello  Changes copied from SEEDtk project.
p3x-eval-sort.pl  1.1  14 months  parrello  Changes copied from SEEDtk project.
p3-blast.pl  1.4  14 months  parrello  Changes copied from SEEDtk project.
p3-rast.pl  1.4  14 months  parrello  Changes copied from SEEDtk project.
p3-pick.pl  1.2  14 months  parrello  Changes copied from SEEDtk project.
p3-count-families.pl  1.1  14 months  parrello  Changes copied from SEEDtk project.
ic50_extract.pl  1.1  14 months  parrello  Changes copied from SEEDtk project.
fasta_dna.pl  1.1  14 months  parrello  Changes copied from SEEDtk project.
p3-get-genome-group.pl  1.4  14 months  parrello  Changes copied from SEEDtk project.
align_fasta.pl  1.4  16 months  golsen  Add support for mafft.
p3x-setup-alignment-sync-dir.pl  1.1  16 months  olson  For P3 fam build, set up sync.dir
verify_genome_directory.pl  1.44  18 months  olson  fix warning output
p3-identical-proteins.pl  1.3  19 months  parrello  Changes copied from SEEDtk project.
p3-feature-gap.pl  1.4  19 months  parrello  Changes copied from SEEDtk project.
p3-project-subsystems.pl  1.2  19 months  parrello  Changes copied from SEEDtk project.
p3-tbl-to-fasta.pl  1.2  19 months  parrello  Changes copied from SEEDtk project.
p3-abstract-clusters.pl  1.2  19 months  parrello  Changes copied from SEEDtk project.
p3-generate-close-roles.pl  1.3  19 months  parrello  Changes copied from SEEDtk project.
p3-signature-peginfo.pl  1.3  19 months  parrello  Changes copied from SEEDtk project.
p3-extract-gto.pl  1.6  19 months  parrello  Changes copied from SEEDtk project.
p3-get-feature-sequence.pl  1.6  19 months  parrello  Changes copied from SEEDtk project.
p3-inAorB.pl  1.3  19 months  parrello  Changes copied from SEEDtk project.
p3-count.pl  1.2  19 months  parrello  Changes copied from SEEDtk project.
p3-inAnotB.pl  1.3  19 months  parrello  Changes copied from SEEDtk project.
p3-aggregate-sss.pl  1.3  19 months  parrello  Changes copied from SEEDtk project.
package_subsystems.pl  1.6  19 months  parrello  Changes copied from SEEDtk project.
p3-aggregates-to-html.pl  1.6  19 months  parrello  Changes copied from SEEDtk project.
p3-kmer-compare.pl  1.2  19 months  parrello  Changes copied from SEEDtk project.
p3-identical-dna.pl  1.3  19 months  parrello  Changes copied from SEEDtk project.
p3-signature-clusters.pl  1.3  19 months  parrello  Changes copied from SEEDtk project.
p3-list-genome-groups.pl  1.3  19 months  parrello  Changes copied from SEEDtk project.
p3-similar-proteins-by-family.pl  1.4  19 months  parrello  Changes copied from SEEDtk project.
p3-inAandB.pl  1.3  19 months  parrello  Changes copied from SEEDtk project.
p3-similar-proteins-by-blast.pl  1.3  19 months  parrello  Changes copied from SEEDtk project.
build_SEED_nr.pl  1.1  20 months  olson  Add SEED NR builder using all_valid_protein_features_in_SEED
p3-get-features-by-sequence.pl  1.2  22 months  parrello  Changes copied from SEEDtk project.
p3-genome-fasta.pl  1.5  22 months  parrello  Changes copied from SEEDtk project.
svr_CS.pl  1.9  22 months  olson  add p3 support
package_fix.pl  1.1  23 months  parrello  Changes copied from SEEDtk project.
p3-tbl-to-html.pl  1.1  23 months  parrello  Changes copied from SEEDtk project.
clean_bad_contigs.pl  1.2  23 months  parrello  Updates from SEEDtk
p3-sequence-profile.pl  1.3  23 months  parrello  Updates from SEEDtk
analyze_package_logs.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
p3x-create-release-dir.pl  1.2  2 years  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 years  olson  Add metadata to the query_cb callback. Also use the return value of query_cb to ...
p3x-compute-patric-update-delta.pl  1.1  2 years  olson  Add metadata to the query_cb callback. Also use the return value of query_cb to ...
rast_compute_specialty_genes.pl  1.6  2 years  olson  Update to use blat and new thresholds.
p3x-write-subsystem-qa.pl  1.1  2 years  olson  New module for patric subsystem QA
p3-mass-cluster-run.pl  1.2  2 years  parrello  Changes copied from SEEDtk project.
p3-gto-dna.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
p3-gto-scan.pl  1.3  2 years  parrello  Changes copied from SEEDtk project.
p3-format-results.pl  1.2  2 years  parrello  Changes copied from SEEDtk project.
p3-genus-species.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
p3-related-by-clusters.pl  1.8  2 years  parrello  Changes copied from SEEDtk project.
p3-closest-seqs.pl  1.2  2 years  parrello  Changes copied from SEEDtk project.
p3-head.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
p3-identify-clusters.pl  1.2  2 years  parrello  Changes copied from SEEDtk project.
p3-generate-clusters.pl  1.4  2 years  parrello  Changes copied from SEEDtk project.
p3-set-to-relation.pl  1.3  2 years  parrello  Changes copied from SEEDtk project.
p3-find-in-clusters.pl  1.1  2 years  parrello  Changes from SEEDtk.
p3-build-kmer-db.pl  1.1  2 years  parrello  Changes from SEEDtk.
p3-function-to-role.pl  1.3  2 years  parrello  Changes from SEEDtk
p3-gto-fasta.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
check_rast.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
p3-login.pl  1.6  2 years  parrello  Changes copied from SEEDtk project.
p3-genome-amr-data.pl  1.2  2 years  parrello  Changes copied from SEEDtk project.
p3-get-contig-data.pl  1.2  2 years  parrello  Changes copied from SEEDtk project.
p3-drug-amr-data.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
gto_crisprs.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
p3-list-feature-groups.pl  1.2  2 years  parrello  Changes copied from SEEDtk project.
p3x-write-family-defs.pl  1.1  2 years  olson  Extract local and global family definition files from full family data.
set-from-subtree.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
fq_to_fa.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
set_by_subtree.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
assemble_selected.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
get_families_kmcl.pl  1.1  2 years  olson  KMCL processing.
km_process_hits_to_regions.pl  1.6  2 years  olson  Fix accumulation of weighted score bug.
core_PGF_stats.pl  1.1  2 years  jdavis  Adding core_PGF_stats.pl
GTO_to_PGF_genome_stats.pl  1.1  2 years  jdavis  Adding GTO_to_PGF_genome_stats.pl
get_core_PGFs.pl  1.1  2 years  jdavis  Adding get_core_PGFs.pl
renumber_seed_dir.pl  1.8  2 years  gdpusch  Somewhat dangerous fix to the sims files
svr_genbank_to_seed.pl  1.4  2 years  gdpusch  Extract RNAs as well as PEGs.
gto_complete_check.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
update_taxonomies.pl  1.9  2 years  olson  Revamp of this script to use efetch utility instead of parsing webpage and to ta...
rapid_propagation4.pl  1.11  2 years  gdpusch  Finally fixed (I hope!) the "Undefined Domain" bug.
delete_fids_from_orgdir.pl  1.2  2 years  gdpusch  Improved command-line argument processing
process_evaluation.pl  1.1  2 years  parrello  Changes copied from SEEDtk project.
pegs_on_contigs.pl  1.2  2 years  parrello  Changes copied from SEEDtk project.
kmer_search.pl  1.26  2 years  olson  Add debug flag
make_predictor_input.pl  1.1  3 years  parrello  Changes copied from SEEDtk project.
run_checkm.pl  1.1  3 years  parrello  Changes copied from SEEDtk project.
make_predictor_input_from_gto.pl  1.1  3 years  parrello  Changes copied from SEEDtk project.
find_bad_contigs.pl  1.1  3 years  parrello  Changes copied from SEEDtk project.
p3x-reduce-families-for-kser.pl  1.1  3 years  olson  P3 utility scripts.
p3x-compare-patric-calls.pl  1.1  3 years  olson  P3 utility scripts.
p3x-split-families.pl  1.1  3 years  olson  P3 utility scripts.
p3x-compare-patric-calls-2.pl  1.1  3 years  olson  P3 utility scripts.
p3x-update-propagated-family-names.pl  1.1  3 years  olson  P3 utility scripts.
p3x-check-mcl-compute-times.pl  1.1  3 years  olson  P3 utility scripts.
p3x-propagate-family-names.pl  1.1  3 years  olson  P3 utility scripts.
p3x-create-split-nr-for-fams.pl  1.1  3 years  olson  P3 utility scripts.
p3x-recall-patric-proteins.pl  1.1  3 years  olson  P3 utility scripts.
p3x-recall-proteins.pl  1.1  3 years  olson  P3 utility scripts.
make_genome_dir_for_close.pl  1.11  3 years  gdpusch  second tweak to avoid $contig=0 errors.
km_pick_best_hit_in_peg.pl  1.4  3 years  olson  Some readability / documentation changes.
get_fam_rel.pl  1.1  3 years  parrello  Changes copied from SEEDtk project.
get_fam_corr.pl  1.1  3 years  parrello  Changes copied from SEEDtk project.
run_all_fam_rel.pl  1.1  3 years  parrello  Changes copied from SEEDtk project.
rebuild_converged_Data.pl  1.7  3 years  olson  Commit updates to kmer build code.
run1_convergence_step.pl  1.7  3 years  olson  Commit updates to kmer build code.
km_build_Data.pl  1.20  3 years  olson  Commit updates to kmer build code.
load_pattyfams.pl  1.1  3 years  olson  pattyfam compute.
SwissProtXML_to_JSON.pl  1.1  3 years  golsen  Create wrapper program SwissProtXML_to_JSON for the XML to JSON; includes abilit...
SwissProtJSON_to_loadfile.pl  1.1  3 years  golsen  Create wrapper program SwissProtXML_to_JSON for the XML to JSON; includes abilit...
patric_call_proteins.pl  1.4  3 years  olson  reduce fig obj creation
svr_submit_RAST_job.pl  1.17  3 years  olson  Add rasttk submission support
export_subsystem.pl  1.1  3 years  olson  Subsystem exporter for NCBI.
svc_fasta_to_md5.pl  1.2  3 years  parrello  Changes copied from SEEDtk project.
build_dnaseq_blastdb.pl  1.1  3 years  olson  New blastdb builders.
build_contigs_blastdb.pl  1.1  3 years  olson  New blastdb builders.
sphinx_index_genome.pl  1.14  3 years  olson  fix indexing bug with unanticipated feature types.
svr_corresponding_genes2.pl  1.7  3 years  olson  Revert to 1.5.
find_close_genomes.pl  1.2  3 years  parrello  Changes copied from SEEDtk project.
call_genome_using_glimmer.pl  1.4  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
svr_seed_to_genbank.pl  1.3  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
diff_tbls.pl  1.2  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
feature_length_histogram.pl  1.4  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
remove_rna_overlaps.pl  1.11  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
make_overlap_report.pl  1.22  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
pull_orfs.pl  1.8  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
renumber_features.pl  1.14  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
rapid_propagation5.pl  1.2  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
find_protein_homologs.pl  1.2  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
find_miscalled_genes.pl  1.5  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
svr_seed_to_embl.pl  1.2  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
FFB2_split_fams_by_size.pl  1.3  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
kmer_guts_net.pl  1.2  3 years  olson  Add sas tag.
annotate-ss-with-pattyfams.pl  1.1  3 years  olson  New scripts.
fast_project.pl  1.3  3 years  olson  bugfix
p3x_kser_parallel_load.pl  1.1  4 years  olson  Script to run a parallel load of kser with given nr data.
split_fasta.pl  1.1  4 years  olson  Script to split a fasta file into chunks of a given size.
k-class-adaboost.pl  1.2  4 years  olson  Bob hacks to Jim's code
get_PATRIC_AMR_genome_list.pl  1.1  4 years  jdavis  adding get_PATRIC_AMR_genome_list.pl
get_PATRIC_AMR_data.pl  1.1  4 years  jdavis  adding get_PATRIC_AMR_data.pl
compare_ec_gary_table.pl  1.1  4 years  redwards  module and scripts to compare EC numbers to what we have in the SEED
ec_compare_sib.pl  1.1  4 years  redwards  module and scripts to compare EC numbers to what we have in the SEED
svr_NCBI_sequence.pl  1.1  4 years  golsen  A script for retrieving sequence and related data from NCBI. Output can be tab d...
match_to_axes.pl  1.7  4 years  golsen  Fixed spelling errors in the documentation.
rast_call_RNAs.pl  1.3  4 years  olson  Propagate production fixes.
rapid_subsystem_inference.pl  1.22  4 years  overbeek  fix duplicate code
tabs2rel.pl  1.4  4 years  parrello  Changes copied from SEEDtk project.
rel2tabs.pl  1.3  4 years  parrello  Changes copied from SEEDtk project.
cs_adjacency_data.pl  1.6  4 years  overbeek  fix tmp on sort
place_properties_on_tree.pl  1.6  4 years  overbeek  BAD BUG
get_merged_families_2.pl  1.1  4 years  olson  Global merge code.
get_merged_families_3.pl  1.1  4 years  olson  Global merge code.
p3_contigs_in_genome.pl  1.1  4 years  olson  initial set of PATRIC data accessors. The p3* scripts have the same interface as...
p3_all_genomes.pl  1.1  4 years  olson  initial set of PATRIC data accessors. The p3* scripts have the same interface as...
p3_all_features.pl  1.1  4 years  olson  initial set of PATRIC data accessors. The p3* scripts have the same interface as...
index_sims_file.c  1.8  4 years  seaver  Fixed buffer overflow in index_sims_file that prevented the indexing of a larger...
translate_fasta_6.c  1.2  4 years  golsen  Fixed issues in correctly printing the descriptions.
get_ON_probes.pl  1.5  4 years  jdavis  updated joses new functional roles
bbh_synteny.pl  1.1  4 years  redwards  adding code to make syntentic plots
svr_RNA_genes.pl  1.6  4 years  golsen  Improve comments.
reps_for_wc.pl  1.2  4 years  jdavis  updated usage statement
get_genome_object_from_seed.pl  1.3  4 years  olson  add pseed
k-class-adaboost-classify.pl  1.1  4 years  jdavis  adding k-class-adaboost-classify.pl
k-class-representative_n_tree_tips.pl  1.1  4 years  jdavis  adding k-class-representative_n_tree_tips.pl
k-class-adaboost-matrix-parallel.pl  1.1  4 years  jdavis  adding k-class-adaboost-matrix-parallel.pl
k-class-get-adaboost-tree-tips.pl  1.1  4 years  jdavis  adding k-class-get-adaboost-tree-tips.pl
k-class-tree-from-contig-dir.pl  1.2  4 years  jdavis  had to strip .pl file extensions in system calls
k-class-get-bork-universals.pl  1.1  4 years  jdavis  This gets a set of universal proteins for a genome using blast
k-class-PSEED-kc.pl  1.1  4 years  jdavis  k-class-PSEED-kc.pl is a program to create a directory of kmer count files from ...
k-class-kc.pl  1.1  4 years  jdavis  Adding k-class-kc.pl, a wrapper of Fangfangs kc.pl code which runs kmc
kmc  1.1  4 years  jdavis  adding kmc
fetch_seed_gto.pl  1.4  4 years  parrello  Changes copied from SEEDtk project.
fast_project_ref_to_GTO.pl  1.1  4 years  parrello  Changes copied from SEEDtk project.
GenomeTypeObject.t  1.1  4 years  olson  Initial genome type object tester
svr_tree_to_html.pl  1.14  4 years  fangfang  add fetch_seed_gto.pl
find_RNA_genes.pl  1.1  4 years  golsen  Make blast+ the default in find_nucleotide_homologs, solving an issue with occas...
parse_genbank.pl  1.34  4 years  gdpusch  Fixed parsing failure in case when TAXONOMY string consists of a single field wi...
start_dbserver.pl  1.3  4 years  golsen  Added the $dont_fork parameter to the start_server call, based upon the value of...
svr_roles_to_subsys.pl  1.3  4 years  redwards  changing the separator in SS classifcations
backfill_gaps.pl  1.21  4 years  gdpusch  Accept as few as a single template if it is in a subsystem.
make_kb_md5.pl  1.1  4 years  disz  New script to create kbstyle md5's
fig.pl  1.157  4 years  overbeek  add change_funcrole
svr_preferred_roles.pl  1.6  4 years  overbeek  translation fixes
make_release.pl  1.5  4 years  olson  Add ProblemSets.current symlink management.
svr_neighbors_of.pl  1.5  4 years  overbeek  error checking
root_at_midpoint.pl  1.1  5 years  overbeek  root a tree at the midpoint
write_go_mappings.pl  1.4  5 years  olson  Specialty protein & PATRIC caller code.
get_PSEED_assignment_updates.pl  1.6  5 years  olson  Specialty protein & PATRIC caller code.
rast_load_specialty_genes.pl  1.2  5 years  olson  Specialty protein & PATRIC caller code.
get_translations_for_genomes.pl  1.1  5 years  overbeek  get translations for a set of genomes
svr_cluster_locations.pl  1.1  5 years  overbeek  compute clusters
svr_fids_to_locations.pl  1.1  5 years  overbeek  get locations of fids
rast_prepare_NR_directory.pl  1.1  5 years  olson  annotate via similarity scripts
generate_kmer_peg_rel.pl  1.1  5 years  olson  Initial commit of Ross kmer compare regions code, coped from ~overbeek/Ross/Gene...
load_kmer_peg_db.pl  1.1  5 years  olson  Initial commit of Ross kmer compare regions code, coped from ~overbeek/Ross/Gene...
get_close_pegs.pl  1.1  5 years  olson  Initial commit of Ross kmer compare regions code, coped from ~overbeek/Ross/Gene...
svr_subsystems_to_roles.pl  1.1  5 years  overbeek  get roles of subsystems
genome_set.t  1.1  5 years  olson  Genome set tests & database initialization script
gset-initdb.pl  1.1  5 years  olson  Genome set tests & database initialization script
get_families.pl  1.14  5 years  olson  Clean up tempdir.
ex_pipeline_ross.pl  1.5  5 years  overbeek  added some documentation
overlap_resolution_test.pl  1.2  5 years  golsen  Add a bunch of options to help in diagnosis, including feature list output and f...
get_families_4.pl  1.9  5 years  olson  Add tempdir()/tempfile() calls to manage create temps in right place. Add status...
svr_quick_assign.pl  1.3  5 years  olson  Add tempdir()/tempfile() calls to manage create temps in right place. Add status...
get_families_2.pl  1.4  5 years  olson  Add tempdir()/tempfile() calls to manage create temps in right place. Add status...
svr_function_of.pl  1.15  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
svr_location_of.pl  1.2  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
SStest.pl  1.1  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
svr_upstream.pl  1.9  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
CS_build_fasta_for_phylogeny.pl  1.6  5 years  overbeek  take gids from genome.names
CS_compute_coupling.pl  1.5  5 years  overbeek  take gids from genome.names
condense_kmer_output.pl  1.2  5 years  overbeek  generalize to kbase
get_families_1.pl  1.9  5 years  overbeek  handle bars in genome ids
svr_psiblast_search.pl  1.28  5 years  fangfang  add core seed db
weak_predictors.pl  1.1  5 years  overbeek  annotate via families and weak predictors
apply_annotations.pl  1.7  5 years  olson  Fix in the case of an empty skiplist.
svr_CS_pipeline.pl  1.6  5 years  overbeek  compute adjacency data for What Changed?
compare_annotation_sets.pl  1.1  5 years  olson  Annotation comparison tool.
svr_assign_using_figfams.pl  1.13  5 years  overbeek  describe output more accurately
get_families_final.pl  1.3  5 years  overbeek  fixed documentation
get_families_3.pl  1.3  5 years  overbeek  fixed documentation
kmer_classifier.pl  1.1  5 years  olson  Add Ross/Jim Davis kmer classifier code.
compute_stats_for_kmer_hits.pl  1.2  5 years  overbeek  handle a strange floating point issue
kp_process_dna_hits.pl  1.4  5 years  olson  Fix regex bug.
kp_process_hits.pl  1.7  5 years  olson  Fix regex bug.
blocked_by.pl  1.1  5 years  overbeek  find out why a kmer was blocked
svr_sphinx_indexing.pl  1.1  5 years  overbeek  add access to sphinx indexes
find_bidir_best_hits.pl  1.1  5 years  fangfang  import Gary's find_bidir_best_hits script
svr_representative_sequences.pl  1.2  5 years  fangfang  add -a n_thread option
pg_build_newick_tree.pl  1.2  5 years  overbeek  use muscle for alignments
get_close_pegs_kmer_memcache.pl  1.2  5 years  olson  put hash size back appropriately
load_kmers_into_memcache.pl  1.2  5 years  olson  memcache kmers code
svr_drug_resistance_proteins.pl  1.3  5 years  fangfang  fix merge conflict
compare_gto_assigned_roles.pl  1.1  5 years  gdpusch  Initial checkin.
compare_gto_called_CDSs.pl  1.1  5 years  gdpusch  Initial checkin.
svr_blast.pl  1.2  5 years  overbeek  compute mean/stddev of positive hits
rs.pl  1.2  5 years  overbeek  compute mean/stddev of positive hits
svr_aligns_with_prot.pl  1.1  5 years  golsen  Provide a command line mechanism to get the alignments associated with one or mo...
rationalize_blast.pl  1.5  5 years  golsen  Fixed one typo in an error message.
seed_job_scheduler.pl  1.4  5 years  olson  add pid file argument
ex_get_adjacency_based_estimates.pl  1.2  5 years  overbeek  minor changes
ex_get_subsystem_based_estimates.pl  1.2  5 years  overbeek  minor changes
ex_split_atomic_regulons.pl  1.3  5 years  overbeek  it is ok to have nonpeg aliases
ex_make_initial_atomic_regulons.pl  1.2  5 years  overbeek  two embarrassing bugs in same_profile
kp_run_tests.pl  1.5  5 years  overbeek  fix pubseed flag
Makefile  1.31  5 years  olson  Fix the broken stuff (bob commented out some lines erroneously)
run_coreseed_to_pubseed_flow.sh  1.1  6 years  olson  Support for annotation flow from CoreSEED to PubSEED.
summarize_classification_data.pl  1.1  6 years  overbeek  summarize classification output
kp_get_properties_next_round.pl  1.1  6 years  overbeek  a little script to make next properties file in iterative training
put_func_on_families_2c.pl  1.1  6 years  overbeek  get funcs
svr_members_of_otu.pl  1.4  6 years  overbeek  add entry for rep
svr_fids_to_ids.pl  1.1  6 years  gdpusch  Initial checkin of script to fetch external ("alias") IDs for a FID.
svr_roles_to_reactions.pl  1.2  6 years  overbeek  get reactions implied by roles
kp_build_Data.pl  1.5  6 years  overbeek  handle frac better
find_SEED_SSU_rRNA_genes.pl  1.7  6 years  golsen  Update the reference RNA module name.
paint_reactions_on_tree_pipeline.pl  1.2  6 years  overbeek  trying to commit a working copy
br_evaluate_properties.pl  1.1  6 years  overbeek  trying to commit a working copy
evaluate_properties.pl  1.1  6 years  overbeek  a tool that uses boolean evaluation
kmer_property_search.pl  1.3  6 years  overbeek  make frac hits for kmer a parameter
pg_get_pegs_in_repeats.pl  1.3  6 years  overbeek  set min overlap to 50
km_build_kmers_part1.pl  1.2  6 years  overbeek  fix test for fI
km_build_function_index.pl  1.1  6 years  overbeek  Release 1.0: see ~overbeek/Ross/LoosenedKmers/bin/Release1.0/bin
km_build_kmers_part2.pl  1.1  6 years  overbeek  Release 1.0: see ~overbeek/Ross/LoosenedKmers/bin/Release1.0/bin
km_build_just_otu_index.pl  1.1  6 years  overbeek  Release 1.0: see ~overbeek/Ross/LoosenedKmers/bin/Release1.0/bin
ex_add_conditions.pl  1.1  6 years  overbeek  add conditions/samples
pg_compute_corr.pl  1.3  6 years  overbeek  handle extraction of genome id better
load_propagation_locks.pl  1.1  6 years  olson  Initialize propagation locks table.
ex_rare_ar_and_pegs.pl  1.1  6 years  overbeek  added steps
ex_fillout_ar_data.pl  1.1  6 years  overbeek  added steps
where_shifts_occurred.pl  1.2  6 years  overbeek  fix child check
svr_mark_tree_states.pl  1.5  6 years  golsen  Fix my comments on rendering.
svr_reaction_gain_loss_table.pl  1.1  6 years  golsen  Tools for mapping reaction presence and absence onto a tree.
pg_pipeline.pl  1.51  6 years  overbeek  readdble.tree is in Analysis
pg_janaka_get_role_reactions_pegs.pl  1.4  6 years  overbeek  get rid of comments on functions
ex_make_on_off_calls.pl  1.3  6 years  overbeek  get locus/peg right
ex_compute_pccs.pl  1.3  6 years  overbeek  add spearman stuff
ex_set_on_off_for_atomic_regulons.pl  1.1  6 years  overbeek  expression pipeline + ato,ic regulons
ex_adjust_peg_on_off.pl  1.1  6 years  overbeek  expression pipeline + ato,ic regulons
pg_add_role_peg.pl  1.4  6 years  overbeek  bad stuff
pg_make_reaction_properties.pl  1.1  6 years  overbeek  make reaction properties to paint tree
label_all_nodes.pl  1.2  6 years  overbeek  unlabel/label
pg_extract_reaction_sets.pl  1.4  6 years  overbeek  fix eol
pg_make_initial_models.pl  1.12  6 years  overbeek  watch out for failing models
svr_get_rep_genomes.pl  1.2  6 years  overbeek  minor fix of documentation
FFB3_get_recent_annotations.pl  1.2  6 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_assemble_translations.pl  1.2  6 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_make_subsys_based_families.pl  1.2  6 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_build_updated_FF.pl  1.5  6 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_construct_assigned_functions.pl  1.2  6 years  olson  FFB3_build_updated_FF: Add --temp to force use of given temp directory Change ha...
FFB3_update_FIGfams.pl  1.2  6 years  olson  Favor non-blank functions in FFB3_update_FIGfams::function_of_family Add new scr...
FFB3_cleanup_families.pl  1.1  6 years  olson  Favor non-blank functions in FFB3_update_FIGfams::function_of_family Add new scr...
check_genomes_by_ribo_proteins.pl  1.2  6 years  overbeek  handle dup assignments
svr_get_all.pl  1.2  6 years  olson  Make array-valued fields be returned as comma-joined.
get_unique_kmers_for_rnaseq.pl  1.3  6 years  overbeek  take in K as a n argument
get_list_of_genomes_to_delete.pl  1.3  6 years  overbeek  more stringent bounds
run_ribo_ratio_against_pubseed.pl  1.1  6 years  overbeek  quality control using ribo proteins
compute_ribo_ratio.pl  1.1  6 years  overbeek  quality control using ribo proteins
compute_ribo_ratio_by_function.pl  1.1  6 years  overbeek  quality control using ribo proteins
build_nr_md5.pl  1.1  6 years  olson  md5 nr builder
pg_intersection.pl  1.1  6 years  overbeek  add Jose stuff
rs_pipeline.pl  1.1  6 years  overbeek  the rna_seq pipeline
rs_create_ref_profile.pl  1.1  6 years  overbeek  the rna_seq pipeline
rs_get_peg_counts.pl  1.1  6 years  overbeek  the rna_seq pipeline
rs_get_rnas.pl  1.1  6 years  overbeek  the rna_seq pipeline
rs_get_intergenic_counts.pl  1.1  6 years  overbeek  the rna_seq pipeline
svr_add_reaction_descriptions.pl  1.1  6 years  overbeek  a tool to add reaction descriptions
pg_compute_traits.pl  1.3  6 years  overbeek  fix to pass2
modelCompare.pl  1.1  6 years  disz  Janaka reaction code
pg_inconsistent_families.pl  1.4  6 years  overbeek  strip comments
pg_get_stats.pl  1.3  6 years  overbeek  fixes due to using nonRAST genomes
get_exemplars_as_needed.pl  1.3  6 years  overbeek  minor fixes
get_dlit_data.pl  1.1  6 years  overbeek  exemplar code
pg_core_families.pl  1.8  6 years  overbeek  minor fix
pg_build_protein_families.pl  1.4  6 years  overbeek  fixes to pan-genera pipeline
pg_build_fasta_for_phylogeny.pl  1.5  6 years  overbeek  updates induced by Bob
seed2ptt.pl  1.2  6 years  redwards  adding alternate genome selections
merge_missing_sims.pl  1.1  6 years  redwards   a set of scripts for adding phage genomes to the seed
update_phage_annotations.pl  1.1  6 years  redwards   a set of scripts for adding phage genomes to the seed
merge_peg_synonyms.pl  1.1  6 years  redwards   a set of scripts for adding phage genomes to the seed
sims_after_adding_genome.pl  1.1  6 years  redwards   a set of scripts for adding phage genomes to the seed
duplicate_genomes.pl  1.1  6 years  redwards   a set of scripts for adding phage genomes to the seed
rewrite_peg_syns.pl  1.1  6 years  redwards   a set of scripts for adding phage genomes to the seed
export_all_viruses.pl  1.1  6 years  redwards   a set of scripts for adding phage genomes to the seed
check_sims_for_added_genome.pl  1.1  6 years  redwards   a set of scripts for adding phage genomes to the seed
add_phage_from_rast.sh  1.1  6 years  redwards   a set of scripts for adding phage genomes to the seed
export_phage_data.pl  1.4  6 years  redwards  a cron job to export phage data
svr_project_by_sr.pl  1.1  6 years  overbeek  project with SRs
FFB2_pull_extreme_FF_members.pl  1.2  6 years  olson  Update to figfam processing
FFB2_merge_and_build_kmers.pl  1.1  6 years  olson  Update to figfam processing
FFB2_update_FIGfams.pl  1.17  6 years  olson  Update to figfam processing
FFB2_get_oligos2.pl  1.4  6 years  olson  Update to figfam processing
FFB3_set_figfam_functions.pl  1.2  6 years  olson  Update to figfam processing
FFB2_make_FF_index.pl  1.3  6 years  olson  Update to figfam processing
FFB2_build_updated_FF.pl  1.24  6 years  olson  Update to figfam processing
delete_functions_for_nonextent_ff.pl  1.1  6 years  overbeek  delete functions for nonexisting families
sr_pipeline.pl  1.3  6 years  overbeek  mixed pipelines
get_rid_of_small_or_too_many_per_FF.pl  1.2  6 years  overbeek  allow short prots in subsys
make_sr_inconsistent_fams.pl  1.1  6 years  overbeek  build input for Bob to display
get_all.pl  1.2  6 years  disz  Fixed the example
pg_function_of.pl  1.2  6 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_adjacency_of_core.pl  1.2  6 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_compute_md5s.pl  1.1  6 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_compute_subsystem_membership.pl  1.1  6 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_make_md5_families.pl  1.5  6 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_process_pubs.pl  1.1  6 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_roles_in_some_but_not_X.pl  1.9  6 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_estimate_alien_pegs.pl  1.3  6 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_form_mobile_element_families.pl  1.3  6 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_events.pl  1.2  6 years  olson  Modifications to pangenome code to move common code to PG.pm.
pg_get_consistency_before_after.pl  1.2  6 years  overbeek  handle no assignments
pg_get_reaction_keys.pl  1.1  6 years  overbeek  add gapfilling
pg_get_reaction_role.pl  1.1  6 years  overbeek  add gapfilling
pg_get_gapfill_reactions.pl  1.1  6 years  overbeek  add gapfilling
pg_get_models.pl  1.1  6 years  overbeek  add gapfilling
pg_get_reactions.pl  1.1  6 years  overbeek  add gapfilling
pg_check_gapfills.pl  1.1  6 years  overbeek  add gapfilling
pg_run_gapfills.pl  1.1  6 years  overbeek  add gapfilling
pg_get_codon_usage_stats.pl  1.1  6 years  overbeek  add codon usage
fast_grep.pl  1.1  6 years  overbeek  example of systead
evaluate_annotation_consistency.pl  1.1  6 years  fangfang  script for evaluating annotation consistency
pg_tabulate_reactions.pl  1.2  6 years  overbeek  compute core reactions
pg_filter_alien.pl  1.1  6 years  overbeek  reorder alien computation
pg_make_reaction_tables.pl  1.1  6 years  overbeek  extract reaction table
pg_submit_to_RAST.pl  1.3  6 years  overbeek  taxon id - not debugged
sketch_tree.pl  1.5  6 years  olson  Revive this script.
solid_rectangles_to_solid_families.pl  1.1  6 years  overbeek  format output
find_new_annotations.pl  1.6  6 years  parrello  Fixed to recover from genomes with missing annotation files.
pg_generate_possible_assignments.pl  1.1  6 years  overbeek  pg pipeline
svr_find_clusters_relevant_to_reaction.pl  1.6  6 years  overbeek  compute correspondences for a pan genome
make_scored_instances.pl  1.5  6 years  overbeek  compute correspondences for a pan genome
svr_close_genomes.pl  1.2  6 years  overbeek  compute correspondences for a pan genome
compute_atomic_regulons.pl  1.3  6 years  overbeek  compute correspondences for a pan genome
svr_coregulated_by_correspondence.pl  1.7  6 years  overbeek  compute correspondences for a pan genome
partition_prots.pl  1.5  6 years  overbeek  compute correspondences for a pan genome
CSA_create_SNP_data.pl  1.7  6 years  overbeek  compute correspondences for a pan genome
pop_vec.pl  1.2  6 years  overbeek  compute correspondences for a pan genome
extract_halo_genomes.pl  1.7  6 years  overbeek  compute correspondences for a pan genome
compute_pc.pl  1.2  6 years  overbeek  compute correspondences for a pan genome
svr_in_fasta.pl  1.1  6 years  overbeek  compute correspondences for a pan genome
ma_pipeline_ecoli.pl  1.3  6 years  overbeek  compute correspondences for a pan genome
pg_add_genomes.pl  1.1  6 years  overbeek  add RAST genomeIDs to genome table
run_anno_to_pubseed_flow.sh  1.6  6 years  olson  fix missing \
summarize_genome_data.pl  1.1  6 years  overbeek  create summary_of_genome data
svr_which_genus_species.pl  1.1  6 years  overbeek  basic kmer validation tools
svr_generate_dna_samples.pl  1.1  6 years  overbeek  basic kmer validation tools
build_solid_set.pl  1.3  6 years  overbeek  avoid including transport or regulatory clusters
pubseed_data_export.pl  1.1  6 years  olson  Data exporter for pubseed.
add_assertions_of_function.pl  1.39  6 years  golsen  Add error report of invalid confidence value. Fix the parsing of roles into the ...
harvest_genomes_from_samples.pl  1.1  6 years  overbeek  possibly buggy - salvaged after the fact
process_otus.pl  1.8  6 years  overbeek  do not use ref in sparse
sparse_genome_sample.pl  1.1  6 years  golsen  A script to provide a set of diverse genomes (< 90% identical) that are similar ...
keep_good_connections.pl  1.3  6 years  overbeek  change definition of required ratio
extract_genomes_from_samples.pl  1.2  6 years  overbeek  needs work on getting rRNAs
tmpred_predictions.pl  1.2  6 years  overbeek  version untied to Sapling
svr_tmpred_predictions.pl  1.2  6 years  overbeek  fix_comment
load_patric_map.pl  1.1  6 years  olson  Load patric mapping data.
svr_current_annotation.pl  1.4  6 years  fangfang  fix bug
check_consistency_of_rectangles.pl  1.1  6 years  overbeek  check consistency of solid rectangles
sort_sets_of_pegs.pl  1.1  6 years  overbeek  sort a set of peg sets
generate_clusters.pl  1.1  6 years  overbeek  program to generate clusters for a reference genome by checking decay rates
svr_project_model.pl  1.2  7 years  overbeek  effectors are not required input
generate_prolog_facts.pl  1.6  7 years  overbeek  no fields with tabs
make_supporting_predicates.pl  1.3  7 years  overbeek  handle minor issue with compound predicate
svr_atomic_reg_coexp.pl  1.1  7 years  overbeek  initial version
svr_taxonomy.pl  1.4  7 years  fangfang  Added flag for taxonomy level
match_to_genome_axes.pl  1.2  7 years  golsen  Updated to use GenomeCodonUsages.pm
match_to_genome_frequencies.pl  1.3  7 years  golsen  Updated to use GenomeCodonUsages.pm
BuildCodonUsageExchAndLoadFiles.pl  1.1  7 years  golsen  Build files to support moving codon usage data into KBase.
svr_ali_to_html.pl  1.4  7 years  fangfang  fixed bug for the no color option by using Gary's new repad_alignment code
alignment_to_html.pl  1.4  7 years  golsen  Add more flexible color by residue: -R ale | default | gde | none
readable_fasta.pl  1.1  7 years  overbeek  initial versions
to_fasta.pl  1.1  7 years  overbeek  initial versions
make_PATRICfams.pl  1.4  7 years  overbeek  minor fix
make_PATRICfams_collapse_md5.pl  1.2  7 years  overbeek  minor fixes
build_PGs_for_OTUs.pl  1.2  7 years  overbeek  fix path
freqs_2_nj_tree.pl  1.3  7 years  golsen  Some minor changes.
freqs_2_dists.pl  1.1  7 years  golsen  Compute pairwise distances between sets of codon usage frequencies.
modal_codon_usage.pl  1.2  7 years  golsen  Add full fasta description line to counts file.
codon_counts_x_and_p.c  1.1  7 years  golsen  Support for codon usage analyses.
filter_codon_counts.pl  1.1  7 years  golsen  Support for codon usage analyses.
gjoseqio.c  1.1  7 years  golsen  Support for codon usage analyses.
gjoseqio.h  1.1  7 years  golsen  Support for codon usage analyses.
codon_freq_eval_2.c  1.1  7 years  golsen  Support for codon usage analyses.
gjoseqlib.c  1.1  7 years  golsen  Support for codon usage analyses.
gjocodonlib.h  1.1  7 years  golsen  Support for codon usage analyses.
gjoseqlib.h  1.1  7 years  golsen  Support for codon usage analyses.
gjocodonlib.c  1.1  7 years  golsen  Support for codon usage analyses.
translate_fasta.c  1.1  7 years  golsen  Support for codon usage analyses.
native_codon_usage.pl  1.1  7 years  golsen  Support for codon usage analyses.
project_codon_usage_onto_axis.c  1.1  7 years  golsen  Support for codon usage analyses.
complement_fasta.c  1.1  7 years  golsen  Support for codon usage analyses.
svr_assign_to_dna_using_figfams.pl  1.18  7 years  olson  add prot length and genus
reindex_sim_btrees.pl  1.1  7 years  olson  new script to update btree indexes of sims files in a genome dir
CSA_ref_vs_ref.pl  1.6  7 years  overbeek  extra comments
correct_frameshifts.pl  1.26  7 years  gdpusch  Grandfather in "-just_mark" in addition to "-justMark".
svr_identical_genomes.pl  1.2  7 years  overbeek  return seed, as well
assign_to_dna_using_kmers.pl  1.6  7 years  redwards  adding details to the assign to DNA for kmer calls
sigs.pl  1.2  7 years  overbeek  slight change of parameters with better tests
find_more_instances_for_veronika.pl  1.1  7 years  overbeek  Fangfang tools to support Veronika
create_ff_covering_skeleton.pl  1.3  7 years  overbeek  remove invocation of representative_sequences
svr_img_analysis.pl  1.5  7 years  parrello  Converted to new interface.
flatten_erdb_xml.pl  1.1  7 years  olson  script to write tabular form of ERDB XML file
assigned_functions_from_rast.pl  1.1  7 years  redwards  adding code to make an assigned_functions file in rast dirs
build_aligns_and_trees_for_seqs.pl  1.2  7 years  fangfang  removed comments
submit_corr_to_server.pl  1.2  7 years  overbeek  fefault value for map submission
get_needed_corr.pl  1.1  7 years  overbeek  for veronika projections
possible_projections.pl  1.1  7 years  overbeek  for veronika projections
publish_subsystems.pl  1.1  7 years  olson  script to programmagically publish a subsystem
daily.pl  1.9  7 years  disz  new right side
to_run_daily.sh  1.4  7 years  disz  Updated to use recent_annotations_by_genome
recent_annotations_by_genome.pl  1.1  7 years  disz  create data for the Daily SEED
submit_corr.pl  1.1  7 years  overbeek  create new saved correspondences
FFB3_merge_families_by_kmers.pl  1.1  7 years  olson  roundup of figfam build changes
get_peg_md5_func_subsystem.pl  1.1  7 years  overbeek  to support assigning FigFam functions
set_figfam_functions.pl  1.1  7 years  overbeek  to support assigning FigFam functions
get_recent_annotations.pl  1.1  7 years  overbeek  to support assigning FigFam functions
svr_align_seqs.pl  1.15  7 years  overbeek  allow option to preserve sequence order
CSA_build_alignments.pl  1.17  7 years  overbeek  allow option to preserve sequence order
run_rabbit_daemon.pl  1.5  7 years  olson  Add memcached support
FFB3_usable_motifs.pl  1.1  7 years  olson  New figfam building code.
FFB3_make_subsys_based_families_2.pl  1.1  7 years  olson  New figfam building code.
FFB3_merge_and_build_kmers.pl  1.1  7 years  olson  New figfam building code.
FFB3_run_tests.pl  1.1  7 years  olson  New figfam building code.
FFB3_load_oligo_index.pl  1.1  7 years  olson  New figfam building code.
FFB3_get_oligos.pl  1.1  7 years  olson  New figfam building code.
FFB3_build_otu_oligos.pl  1.1  7 years  olson  New figfam building code.
FFB3_families_to_fasta.pl  1.1  7 years  olson  New figfam building code.
FFB3_compare_tests.pl  1.1  7 years  olson  New figfam building code.
FFB3_build_ff_indexes.pl  1.1  7 years  olson  New figfam building code.
FFB3_create_binary_kmers.pl  1.1  7 years  olson  New figfam building code.
FFB3_package_figfams.pl  1.1  7 years  olson  New figfam building code.
FFB3_get_gs_oligos.pl  1.1  7 years  olson  New figfam building code.
FFB3_build_ff_oligos.pl  1.1  7 years  olson  New figfam building code.
FFB3_run_parallel_usable_motifs.pl  1.1  7 years  olson  New figfam building code.
seed2genbank.pl  1.6  7 years  redwards  adding SOURCE and taxonomy information
get_all_dlits.pl  1.2  7 years  golsen  Fix some off by one errors.
svr_make_pan_genome_prot_families.pl  1.10  7 years  overbeek  fix bad comments
get_all_annotations.pl  1.1  7 years  disz  New scripts to load the function audit trail database
load_function_transition_table.pl  1.1  7 years  disz  New scripts to load the function audit trail database
trail.pl  1.1  7 years  disz  New scripts to load the function audit trail database
make_indexes.pl  1.18  7 years  golsen  Fixed bugs that made script crash with older SEED layout.
recall_pegs.pl  1.2  7 years  overbeek  add blocked robot
conditionally_assign.pl  1.6  7 years  golsen  Just a little more testing and nicer useage info.
svr_genome_of.pl  1.1  7 years  overbeek  genome of feature
svr_complex_to_reaction.pl  1.1  7 years  parrello  New script to connect complexes to reactions.
svr_role_to_complex.pl  1.1  7 years  parrello  New script to map roles to complexes.
svr_function_to_role.pl  1.1  7 years  parrello  New script for converting functions to roles.
svr_all_roles_used_in_models.pl  1.1  7 years  parrello  New command for roles found in models.
svr_all_complexes.pl  1.1  7 years  parrello  New script to return all complexes.
build_nap_alignments.pl  1.4  7 years  overbeek  place the PseudoGene alignments
create-new-page.pl  1.6  7 years  disz  added sopme more use lines
exp_pc_compute.pl  1.10  7 years  parrello  Updated to process directories in order.
call_coregulated_clusters_on_chromosome.pl  1.8  7 years  overbeek  reduce threshhold on pcc from 0.7 to 0.6
svr_regulons_to_fids.pl  1.1  7 years  parrello  New script to get the features in a regulon.
svr_fids_to_regulons.pl  1.1  7 years  parrello  New script to find regulons for features.
svr_md5_of_prot.pl  1.4  7 years  overbeek  get rid of debugging statement
svr_all_genomes.pl  1.3  8 years  overbeek  support restriction to proks
svr_dlits.pl  1.1  8 years  parrello  New script to call dlits_for_ids
svr_pegs_with_evcode.pl  1.2  8 years  overbeek  must have genomes specified
svr_get_ali_and_tree.pl  1.1  8 years  overbeek  get alignment and tree from seq(s)
gather_pg_sets.pl  1.3  8 years  overbeek  minor fixes
svr_inconsistent_sets.pl  1.5  8 years  overbeek  minor fixes
make_PG.pl  1.3  8 years  overbeek  clarify condition
svr_submit_correspondences.pl  1.2  8 years  parrello  Enhanced to handle Ross's alternate directory structure for correspondence maps....
sort_by_function.pl  1.2  8 years  disz  Fixed find old function
svr_call_rnas.pl  1.2  8 years  overbeek  fix pod doc
initialize_ann_and_ev.pl  1.4  8 years  olson  fix typo
svr_run_RAST_jobs.pl  1.7  8 years  olson  Add kmerDataset selection support.
svr_get_default_dataset.pl  1.1  8 years  olson  script to retrieve the name of the current default kmer datasets
svr_delete_from_set.pl  1.1  8 years  disz  New persistent set svr scripts
svr_delete_set.pl  1.1  8 years  disz  New persistent set svr scripts
svr_put_set.pl  1.1  8 years  disz  New persistent set svr scripts
svr_get_set.pl  1.2  8 years  disz  New persistent set svr scripts
svr_enumerate_sets_by_owner.pl  1.1  8 years  disz  New persistent set svr scripts
svr_create_set.pl  1.1  8 years  disz  New persistent set svr scripts
just_inconsistent_sets.pl  1.1  8 years  overbeek  show inconsistyent sets
svr_sets_by_owner.pl  1.1  8 years  disz  enumerate sets by owner
svr_subsystem_classification.pl  1.1  8 years  gdpusch  Initial prototype checkin, still missing bells and whistles.
svr_cdd_scan.pl  1.3  8 years  fangfang  retrieve non-specific hits for full mode
svr_mapped_genomes.pl  1.4  8 years  parrello  Fixed a leftover hack.
EmergencySubsystemFix.pl  1.2  8 years  parrello  Bug fix in index_subsystems call.
to_run_new_genomes.sh  1.3  8 years  disz  Added source of environment
process_genomes.pl  1.1  8 years  disz  Format new genomes for the Daily SEED
index_genome.pl  1.1  8 years  olson  Add index_genome.pl that will create the SEED data structures for a new SEED dir...
run_all_inference.pl  1.2  8 years  olson  Run on all genomes; update anything either missing a subsystems file or that hav...
rapid_subsystem_inference_batch.pl  1.4  8 years  olson  Fix null-key bug
svr_aliases_of.pl  1.7  8 years  parrello  Fixed for better flow control.
svr_export_as_seed_dir.pl  1.3  8 years  olson  bugfix, get all subsystem records.
CSA_collapse_repeats.pl  1.3  8 years  overbeek  make sorts in local dir, not /tmp
CSA_make_unique_kmers.pl  1.4  8 years  overbeek  make sorts in local dir, not /tmp
CSA_predict_features_based_on_refs.pl  1.1  8 years  overbeek  minor fixes
CSA_second_pass.pl  1.4  8 years  overbeek  fix coordinates within alignments
CSA_close_strains.pl  1.8  8 years  overbeek  sort space in this directory
CSA_merge_estimates.pl  1.8  8 years  overbeek  add translations to features
svr_sketch_tree.pl  1.4  8 years  golsen  Trivial change to the usage information.
CSA_get_close_strain_annotations.pl  1.5  8 years  overbeek  spelling errors
sort_by_annotator.pl  1.2  8 years  disz  Fixed bad links
svr_inherit_annotations.pl  1.3  8 years  gdpusch  Saved ouput of ID mapping to file "inheritance.id_map," and added some bulletpro...
build_sas_distro.pl  1.11  8 years  devoid  Making changes to build distro to support ModelSEED packages. Modified Files: F...
build_dtr_distro.pl  1.4  8 years  devoid  Making changes to build distro to support ModelSEED packages. Modified Files: F...
CSA_first_pass.pl  1.4  8 years  overbeek  remove dependency on BasicLocation
build_sas_distro_from_cvs.pl  1.5  8 years  olson  Revert to the versions from backups.
CSA_layout.pl  1.2  8 years  overbeek  make part of myRAST distribution
CSA_get_repeat_dna.pl  1.2  8 years  overbeek  make part of myRAST distribution
CSA_make_conn.pl  1.2  8 years  overbeek  make part of myRAST distribution
CSA_filter_unique.pl  1.2  8 years  overbeek  make part of myRAST distribution
CSA_make_contig_index.pl  1.2  8 years  overbeek  make part of myRAST distribution
CSA_gather_mapped_objects.pl  1.2  8 years  overbeek  make part of myRAST distribution
svr_find_protein.pl  1.2  8 years  parrello  Fixed the error reporting.
apply_automatic_subsystem_updates.pl  1.1  8 years  olson  Scripts to run rapid_subsystem_inference_batch across all genomes, and to apply ...
svr_inherit_aliases.pl  1.5  8 years  gdpusch  Fixed mapping failure.
add_dlits.pl  1.1  8 years  parrello  New script for adding protein-based Dlits.
index_subsystems.pl  1.15  8 years  olson  add nonaux role index
seed2txt.pl  1.1  8 years  olson  create spreadsheet of SEED org
svr_file_to_spreadsheet.pl  1.3  8 years  olson  If -u url flag is added, add links to pegs.
svr_fasta_to_md5.pl  1.1  8 years  parrello  New script for computing MD5s from FASTA protein sequences.
svr_update_corr_maps.pl  1.2  8 years  overbeek  minor fix
svr_fids_for_md5.pl  1.1  8 years  parrello  New method to return FIG IDs for a protein given its MD5.
load_md5_alignment.pl  1.1  8 years  parrello  New script to load alignments into the PUBSEED server.
init_FIG.pl  1.13  8 years  olson  fixes for when dbhost is set
run_rabbit_daemon_set.pl  1.3  8 years  olson  remove debug
svr_gap_filled_reactions_and_roles.pl  1.5  8 years  devoid  fixing some problems with authentication, error reporting
annotation_counts.pl  1.2  8 years  disz  Check in coming dates
svr_all_features.pl  1.7  8 years  olson  Deobfuscate the command line logic. Submit requests in chunks so as to not be pa...
analyze_loose_sets.pl  1.3  8 years  parrello  Added CSV output that can be used to generate a spreadsheet of recommended funct...
convert_tbl_files.pl  1.1  8 years  parrello  New script for fancy tbl file conversion.
remove_multiple_occurring_probes.pl  1.2  8 years  olson  exp fixes
process_one_exp_dir.pl  1.4  8 years  olson  fix typo
make_coreg_conjectures_based_on_subsys.pl  1.6  8 years  overbeek  allow working from estiomates of SS
svr_find_fused_genes.pl  1.3  8 years  fangfang  updated POD
svr_link_to_compare_regions.pl  1.4  8 years  fangfang  fixed typo in $genomeH
svr_cohesion_groups.pl  1.4  8 years  fangfang  update
FFB2_make_family_vector.pl  1.1  8 years  olson  compute family.vector.def for a figfam direcotry.
svr_is_hypo.pl  1.3  8 years  overbeek  minor fixes
svr_subsystem_roles.pl  1.2  8 years  overbeek  allow ss from stdin
build_sets_from_clusters.pl  1.2  8 years  parrello  Minor fixes for debugging.
corr_build_connections.pl  1.1  8 years  parrello  New stuff for Salmonella sets.
svr_rRNA.pl  1.2  8 years  fangfang  update pod
svr_atomic_regulons.pl  1.1  8 years  parrello  Added to allow retrieval of pegs in atomic regulons.
svr_ss_classes.pl  1.1  8 years  parrello  Added to get classification data for subsystems.
svr_all_experiments.pl  1.1  8 years  parrello  Added to get experiments for each genome.
svr_pegs_in_subsystems.pl  1.7  8 years  parrello  Fixed to process 10 subsystems at a time, reducing the chances of a timeout.
svr_scanN.pl  1.1  8 years  overbeek  scanning utilities
svr_scanP.pl  1.2  8 years  overbeek  add a little documentation
svr_corr_by_exp.pl  1.5  8 years  parrello  Changed to batch the input instead of slurping it.
svr_get_coupling_data.pl  1.2  8 years  overbeek  must have -d
svr_motif.pl  1.4  8 years  fangfang  simplify code
svr_neighborhood_of_role.pl  1.3  8 years  parrello  Converted to use chemistry data instead of the models.
svr_functionally_coupled.pl  1.2  8 years  overbeek  add cutoffs
svr_expressed_genes_in_range.pl  1.1  8 years  parrello  Added for looking at genes that are never or always expressed.
svr_missing_roles.pl  1.2  8 years  overbeek  added -g genome
svr_reaction_description.pl  1.3  8 years  parrello  Added -f flag.
make_probes_to_genes.pl  1.8  8 years  dejongh  check for same contig when matching probe to peg
compute_atomic_regulons_for_dir.pl  1.2  8 years  overbeek  loosen threshhold of mismatches
filter_and_merge_gene_sets.pl  1.2  8 years  overbeek  merge is better
at.pl  1.3  8 years  fangfang  update
svr_tree.pl  1.10  8 years  fangfang  add parallel support for bootstrap
svr_exp_genomes.pl  1.1  8 years  parrello  New script to list expression-data genomes.
svr_spreadsheet_to_file.pl  1.2  8 years  disz  Fixed missing file error message
svr_role_to_pegs.pl  1.3  8 years  overbeek  mispelled genome with bad consequences
svr_neighboring_reactions.pl  1.2  8 years  overbeek  minor fixes
svr_all_models.pl  1.2  8 years  overbeek  keep only Seed models
svr_reactions_in_model.pl  1.1  8 years  parrello  New script for Ross.
svr_reactions_to_roles.pl  1.1  8 years  parrello  New chemistry-based scripts.
svr_all_reactions.pl  1.1  8 years  parrello  New chemistry-based scripts.
svr_coupled_reactions.pl  1.1  8 years  parrello  New chemistry-based scripts.
svr_trim_ali.pl  1.10  8 years  fangfang  fix description field in trim html
RunRMA.R  1.5  8 years  dejongh  preallocate no_match_pm_mm; delete no_match row at end
update_OTUs.pl  1.5  8 years  overbeek  fix OTU update to use gary olsen sequence grouping script
svr_find_hypos_for_cluster.pl  1.1  8 years  overbeek  find hypotheticals associated with clusters
GeneSet_P_Values.R  1.3  8 years  dejongh  fixes
add_to_alignment.pl  1.8  8 years  golsen  Fix the libraries used for I/O.
run_muscle.pl  1.3  8 years  golsen  Update libraries used.
svr_add_lengths_to_blast.pl  1.1  8 years  overbeek   simple utility to add sequence lengths to m8 blast output
find_genes_based_on_kmers.pl  1.9  8 years  olson  More fixups.
compute_PSEED_reconstructions.pl  1.2  8 years  olson  More fixups.
FFB2_usable_motifs2.pl  1.3  8 years  olson  Update to figfam build code
FFB2_load_memcache.pl  1.7  8 years  olson  Update to figfam build code
FFB2_run_tests.pl  1.3  8 years  olson  Update to figfam build code
FFB2_compare_tests.pl  1.4  8 years  olson  Update to figfam build code
FFB2_create_binary_kmers.pl  1.6  8 years  olson  Update to figfam build code
svr_taxonomically_related_genomes.pl  1.10  8 years  fangfang  update POD
svr_just_ends.pl  1.3  8 years  redwards  increasing min length to 2000 so that you have two ends!
accumulate_pegs_to_scenario_paths.pl  1.1  8 years  dejongh  determine which pegs in an organism are involved in which scenario paths
svr_translations_of.pl  1.6  8 years  golsen  Add an option of genome names in the output. Clean up the way functions are adde...
jgi_data_merge.pl  1.2  8 years  golsen  Fix the taxonomy to use NCBI full taxonomy if TAXONOMY does not exist.
load_attributes.pl  1.46  8 years  redwards  changing the attribute of the genome table
fetch_models_for_genomes.pl  1.1  8 years  fangfang  initial import
svr_NCBI_taxonomy.pl  1.2  8 years  golsen  Add more formats in which abbreviated lineages can be returned. Add long form of...
index_translation_files.c  1.8  8 years  redwards  ignoring stops
index_contigs.pl  1.12  8 years  redwards  not reopening a file twice!
flatten_attribute_files.pl  1.2  8 years  redwards  working on all subdirectories, not just a set of them
compute_translation_MD5.c  1.3  8 years  redwards  ignoring stops
load_atomic_regulons.pl  1.1  8 years  olson  initial atomic regulon table loader
RunRMA_SIF_format.R  1.1  8 years  olson  SIF-processing run-rma.
make_ma_html.pl  1.2  8 years  overbeek  minor fixes
mark_genome_as_phage.pl  1.1  8 years  redwards  two phage specific scripts
SplitGeneSets.R  1.2  8 years  olson  Update to expression pipeline code
Pipeline.R  1.4  8 years  olson  Update to expression pipeline code
svr_fasta.pl  1.14  8 years  overbeek  wrap the seq into 60-char lines
load_peg_mapping.pl  1.12  8 years  olson  Caching / FCGI speedup modifications.
svr_with_close_blast_hits.pl  1.1  8 years  overbeek  a utility to find close hits
svr_cluster_pegs.pl  1.1  8 years  overbeek  two small utilities
promote_orfs_to_pegs.pl  1.15  8 years  gdpusch  Code restructured, and modified to fail gracefully if there are no closest genom...
FFB2_merge_families_based_on_genus_groups.pl  1.3  8 years  olson  Big round of figfam update changes
FFB2_make_subsys_based_families.pl  1.3  8 years  olson  Big round of figfam update changes
svr_summarize_protein_families.pl  1.2  8 years  overbeek  minor changes
svr_split_fams.pl  1.1  8 years  overbeek  minor changes
svr_seed_to_table.pl  1.3  8 years  gdpusch  Fixed typo in POD section.
cluster_exp.pl  1.1  9 years  overbeek  cluster experiments into states
FFB2_get_oligos.pl  1.10  9 years  disz  FigFam 6 digit problem
build_new_figfam_release.pl  1.5  9 years  disz  FigFam 6 digit problem
build_prok_nonff_fasta.pl  1.4  9 years  disz  FigFam 6 digit problem
fc_figfams.pl  1.3  9 years  disz  FigFam 6 digit problem
ff.pl  1.7  9 years  disz  FigFam 6 digit problem
figfam.pl  1.23  9 years  disz  FigFam 6 digit problem
find_neighbors.pl  1.39  9 years  disz  FigFam 6 digit problem
find_poss_errs.pl  1.3  9 years  disz  FigFam 6 digit problem
generate_partitionsP.pl  1.6  9 years  disz  FigFam 6 digit problem
generate_partitions_worker.pl  1.4  9 years  disz  FigFam 6 digit problem
initialize_figfams.pl  1.12  9 years  disz  FigFam 6 digit problem
install_partitions.pl  1.5  9 years  disz  FigFam 6 digit problem
make_figfam_tree.pl  1.2  9 years  disz  FigFam 6 digit problem
make_figfam_tree_worker.pl  1.2  9 years  disz  FigFam 6 digit problem
test_figfam_placement_into_families.pl  1.10  9 years  disz  FigFam 6 digit problem
rapid_propagation_plasmid.pl  1.22  9 years  disz  FigFam 6 digit problem
seed2tbl.pl  1.3  9 years  disz  FigFam 6 digit problem
svr_co_occurrence_evidence.pl  1.4  9 years  disz  FigFam 6 digit problem
FFB2_create_binary_relationships.pl  1.1  9 years  olson  New FIGfam merge code.
FFB2_compute_relationships_for_genera.pl  1.1  9 years  olson  New FIGfam merge code.
FFB2_genome_group_pipeline.pl  1.1  9 years  olson  New FIGfam merge code.
filter_trunc_and_fs.pl  1.2  9 years  olson  Add SeedUtils::map_to_families for iterating over families.2c files. Make filte...
svr_find_regulatory_proteins.pl  1.1  9 years  overbeek  a simple tool to find potential regulatory proteins
svr_possible_joins.pl  1.1  9 years  overbeek  tools to try to bridge contigs
svr_intergenic_regions.pl  1.1  9 years  parrello  New script to find intergenic regions.
svr_tab2html.pl  1.5  9 years  gdpusch  Fixed a bug I introduced, and added a "--border" option to the table.
FFB2_usable_motifs.pl  1.4  9 years  olson  Update to FF processing
FFB2_merge_oligos.pl  1.4  9 years  olson  Update to FF processing
FFB2_families_in_subsystems.pl  1.1  9 years  olson  Update to FF processing
FFB2_xy.pl  1.1  9 years  olson  Update to FF processing
FFB2_validate_families.pl  1.1  9 years  olson  Update to FF processing
FFB2_install_kmers.pl  1.2  9 years  olson  Update to FF processing
sequence_length_histogram.pl  1.6  9 years  olson  Include in SAS
svr_genome_statistics.pl  1.2  9 years  parrello  Added genome name to the POD.
svr_cut_domain.pl  1.1  9 years  overbeek  cut domains from sequences
blast2gff.pl  1.23  9 years  redwards  adding an option for gziped files
svr_figfams_to_ids.pl  1.6  9 years  parrello  Added "roles_to_subsys", sped up "figfams_to_ids", fixed pod for "mapped_genomes...
svr_align_using_muscle.pl  1.2  9 years  gdpusch  Fixed incorrect function names.
svr_ids_to_figfams.pl  1.8  9 years  overbeek  fixes to documentation
svr_reroot_tree.pl  1.3  9 years  overbeek  fix typo
svr_corresponding_genes.pl  1.24  9 years  overbeek  fix command line arguments
svr_compare_feature_tables.pl  1.7  9 years  gdpusch  Fixed typo in variable-name
svr_by_taxonomy.pl  1.3  9 years  overbeek  fix parameter passing
svr.pl  1.2  9 years  olson  add . to include path
svr_aliases_to_pegs.pl  1.1  9 years  parrello  New script for Ross
svr_otus.pl  1.3  9 years  overbeek  minor fixes
svr_insert_seqs_into_alignment.pl  1.2  9 years  fangfang  take advantage of gjoseqlib's flexible API to implicitly interact with STDIN/STD...
modify_tree.pl  1.1  9 years  golsen  A general purpose tree modification utility.
rapid_propagation3.pl  1.10  9 years  olson  Support family determiantion.
update_sims2.pl  1.6  9 years  olson  updated code
update_PSEED_subsystems.pl  1.3  9 years  olson  add doc
svr_evidence.pl  1.1  9 years  disz  New svr script to get evidence code
svr_keep_only.pl  1.1  9 years  overbeek  support filtering on function or role
svr_sims2html.pl  1.6  9 years  golsen  Add pod documentation.
svr_tips_of_tree.pl  1.2  9 years  overbeek  add correspondence translation
svr_call_pegs.pl  1.2  9 years  overbeek  fix POD stuff
svr_oligomer_similarity.pl  1.1  9 years  overbeek  compute oligo similarities
generate_ilits.pl  1.3  9 years  olson  fix for FFs changes
compute_figfam_assignments.pl  1.2  9 years  olson  Clean up debugging, write concatenated output file.
ma_pipeline.pl  1.15  9 years  overbeek  get rid of RMA Key
compute_fasta_lengths.pl  1.1  9 years  olson  Precompute fasta lengths for the non-FF nr.
get_coupling_values.pl  1.3  9 years  overbeek  get rid of extraneous routine
svr_fc_figfams.pl  1.3  9 years  overbeek  sort by score
svr_ids_to_subsystems.pl  1.6  9 years  disz  Added stderr output for non-matches
to_genbank.pl  1.7  9 years  gdpusch  Fixed bug handling 5S.
macapp_files_to_genome_dir.pl  1.2  9 years  olson  Banish cp.
svr_metabolic_reconstruction.pl  1.5  9 years  olson  bah, fix paste error
get_neighbors_and_corr_to_ref.pl  1.7  9 years  olson  remove cat and shell usage.
svr_genbank_to_table.pl  1.2  9 years  gdpusch  Added various alias IDs to output.
svr_genome_functions.pl  1.3  9 years  overbeek  sort by feature id
extract_metagene_contigs.pl  1.12  9 years  gdpusch  Updated search for executables to revised software environment.
svr_subsystem_genomes.pl  1.1  9 years  parrello  Discrimination functions support scripts.
svr_discriminating_functions.pl  1.3  9 years  parrello  Discrimination functions support scripts.
FFB2_compare_to_anno3.pl  1.2  9 years  olson  fixes for release names
svr_subsystem_spreadsheet.pl  1.1  9 years  parrello  subsystem download scripts.
svr_figfam_functions.pl  1.2  9 years  parrello  Added option to get all the FIGfams.
svr_contigs_in_genome.pl  1.3  9 years  parrello  Added support for specifying input IDs on the command line.
svr_distinct_otus.pl  1.4  9 years  parrello  Added support for specifying input IDs on the command line.
assess_gene_call_quality.pl  1.14  9 years  olson  don't write the overlap report to metadata log; it is very large.
merge_missing_gene_output.pl  1.3  9 years  olson  bugfix
find_missing_genes.pl  1.10  9 years  olson  more RAST fixes (some of these may need to be backported to use the SAP version ...
svr_dna_seq.pl  1.2  9 years  parrello  More server script stuff.
svr_closest_genes.pl  1.1  9 years  parrello  More server script stuff.
index_translations.pl  1.24  9 years  olson  Add index on fileno.
svr_subsystem_genome_data.pl  1.1  9 years  parrello  More server scripts.
svr_ach_lookup.pl  1.10  9 years  parrello  More server script stuff. Thought I'd already installed these last week...
svr_figfam_fasta.pl  1.5  9 years  parrello  More server script stuff. Thought I'd already installed these last week...
remove_embedded_pegs.pl  1.19  9 years  gdpusch  Modified to use Kmers.
svr_summarize_contigs.pl  1.2  9 years  parrello  New script, some documentation fixes.
svr_gene_data.pl  1.3  9 years  parrello  First round of script updates & additions for tutorial.
rapid_propagation2.pl  1.5  9 years  gdpusch  Minor cosmetic changes.
FFB2_xx.pl  1.1  9 years  olson  Bunch of figfam generation optimizations.
FFB2_get_prots.pl  1.3  9 years  olson  Bunch of figfam generation optimizations.
FFB2_build_ff_indexes.pl  1.1  9 years  olson  Rollup of figfam update fixes
svr_summarize_MG_output.pl  1.4  9 years  overbeek  extend the number of digits in the fraction of the total
svr_determine_sets_of_related_contigs.pl  1.4  9 years  parrello  Documentation fixes.
svr_all_figfams.pl  1.2  9 years  parrello  Documentation fixes.
filter_on_known.pl  1.1  9 years  overbeek  filter pegs with no raw data
CheckCELfiles.R  1.1  9 years  olson  R script to find chip name from CEL files
ma_pipeline_shewanella.pl  1.6  9 years  overbeek  fixes to pipeline
EcoliRMA.R  1.2  9 years  overbeek  from Matt
server_paper_example7.pl  1.4  9 years  chenry  Corrected a few bugs in the example script.
EmergencyMapFlipper.pl  1.2  9 years  parrello  *** empty log message ***
merge_gene_sets.pl  1.1  9 years  overbeek  code from Hope
ShewanellaRMA.R  1.1  9 years  overbeek  code from Hope
FIGMODELscheduler.pl  1.3  9 years  chenry  Switched over the PPO as the system for holding the job queue tables.
svr_copy_to_RAST_dir.pl  1.3  9 years  olson  fix
server_paper_example6.pl  1.3  9 years  parrello  Fixed for server paper.
server_paper_example4.pl  1.3  9 years  parrello  Fixed to use the correct servers.
server_paper_example1.pl  1.12  9 years  parrello  Documentation fix for server paper.
run_glimmer3.pl  1.14  9 years  parrello  Added "-verbose" option so tracing can be turned on from the servers.
load_kegg.pl  1.15  9 years  dejongh  Fix KEGG location
wb.pl  1.1  9 years  overbeek  workbench for alignments and trees
build_all_prok_seqs.pl  1.1  9 years  overbeek  get all protein sequences for complete prokaryotic genomes
exec-cgi.pl  1.1  9 years  olson  cgi executor for mac rast
valid_fasta_file.pl  1.1  9 years  olson  Check to ensure a fasta file is valid.
svr_protein_assertions.pl  1.6  9 years  disz  CHanged ACHserver to SAPserver and fixed processing of return values
svr_all_subsystems.pl  1.9  9 years  parrello  Fixed POD errors. Added examples.
svr_in_runs.pl  1.5  9 years  parrello  Fixed POD errors. Added examples.
update_kegg_data.pl  1.6  9 years  dejongh  removed comment
find_genes_based_on_neighbors_par.pl  1.1  9 years  olson  parallel version of find_genes_based_on_neighbors
update_hope_info.pl  1.4  9 years  dejongh  added comments
check_hope_info.pl  1.8  9 years  dejongh  updates to check for invalid maps and reaction/ec mismatches
svr_update_assignments.pl  1.3  9 years  gdpusch  Fixed typo.
svr_column_of_subsystem.pl  1.1  9 years  olson  server script to pull a subsystem colum
svr_status_of_RAST_job.pl  1.4  9 years  olson  add url argument
assign_using_kmers.pl  1.8  9 years  olson  Add support for explicitly specifying FRI.db, setI.db, table.binary
server_paper_figure2.pl  1.2  9 years  parrello  Removed genetic codes so program fits better on a page.
server_paper_example5.pl  1.3  9 years  disz  Switched to ANNO server
server_paper_example2.pl  1.7  9 years  disz  Changed to use ANNO server
clustered_hypotheticals.pl  1.2  9 years  overbeek  major rewrite
svr_similar_to.pl  1.2  9 years  parrello  Fixed POD errors.
call_genes.pl  1.4  9 years  olson  fix ANNOserver args
find_rnas.pl  1.2  9 years  olson  fix ANNOserver args
svr_SAP.t  1.4  9 years  olson  update tests
svr_scripts.t  1.2  9 years  olson  updated tests
glue_tbl_to_metabolic_reconstruction.pl  1.1  9 years  olson  more anno server fixes, add some missing files
svr_fig_id_corr.pl  1.4  9 years  overbeek  add -precise option
server_paper_example3.pl  1.5  9 years  disz  converted to new SAP server
identify_organism.pl  1.2  9 years  olson  changes for new server stuff
svr_ACH.t  1.1  9 years  olson  new tests
analyze_kmer_assignments.pl  1.1  9 years  olson  new script to compare output of assign_using_kmers to current SEED assignments
svr_kill_RAST_job.pl  1.4  9 years  olson  fix usage message
FFB2_load_oligo_index.pl  1.1  9 years  overbeek  new scripts for updating FIGfams and Kmer tables
FFB2_get_prot_gs_oligos.pl  1.1  9 years  overbeek  new scripts for updating FIGfams and Kmer tables
genbank2fasta.pl  1.2  10 years  redwards  correcting ORIGIN regexp
find_genes_based_on_neighbors.pl  1.24  10 years  olson  Switch to FFs and FF instead of FigFams and FigFam
find_neighbors_using_figfams.pl  1.11  10 years  olson  Switch to FFs and FF instead of FigFams and FigFam
find_genes_in_families.pl  1.22  10 years  olson  Switch to FFs and FF instead of FigFams and FigFam
rep_sets.pl  1.1  10 years  disz  Old code finally checked in to create representative sets
form_clusters.pl  1.2  10 years  parrello  Final Server updates.
svr_delete_RAST_job.pl  1.3  10 years  olson  Fix 666666 problem. Add support for using the test server.
svr_retrieve_RAST_job.pl  1.3  10 years  olson  Misc server fixes
pegs_in_subsystems.pl  1.8  10 years  overbeek  fix documentation
get_genomes_from_ncbi.pl  1.1  10 years  wilke  *** empty log message ***
gather_genome_info.pl  1.2  10 years  olson  Add more data gathering
make_partition_reps_worker.pl  1.3  10 years  arodri7  commit change
install_partition_reps.pl  1.2  10 years  arodri7  commit change
make_partition_repsP.pl  1.4  10 years  arodri7  commit change
assign_using_ff.pl  1.9  10 years  arodri7  commit changes
cleanup_figfams_updates.pl  1.1  10 years  arodri7  commit changes
submit_ff_test.pl  1.6  10 years  arodri7  commit changes
figfam_subsystems.pl  1.2  10 years  arodri7  commit changes
make_subsys_based_families2.pl  1.1  10 years  arodri7  commit changes
propagate_subsys_changes_to_figfams.pl  1.12  10 years  arodri7  commit changes
compare_figfam_release_results.pl  1.5  10 years  arodri7  commit changes
figfam_quality_control.pl  1.8  10 years  arodri7  commit changes
update_FIGfams.pl  1.12  10 years  arodri7  commit changes
get_fasta_for_tbl_entries.pl  1.11  10 years  gdpusch  Modified to remove complaints about uninitialed values when TBL entry does not c...
trim_sequences.pl  1.11  10 years  overbeek  fixes bug in handling multidomain prots
check_consistency_of_sample.pl  1.7  10 years  redwards  correcting looping through parts of the genomes
blastp_pseq.pl  1.6  10 years  redwards  adding a default cutoff
to_prodom.pl  1.7  10 years  olson  fix updated URL
pubbed_fids.pl  1.1  10 years  parrello  New script to find features with publications attached.
split_sequences_into_sets.pl  1.5  10 years  overbeek  handle asym connections
blastP.pl  1.1  10 years  olson  Switch to using assign_functions_to_prot_set in assign_using_kmers.pl. Add blast...
load_wikipedia.pl  1.1  10 years  olson  Wikipedia cache loader.
meta.pl  1.12  10 years  jared  added update_path
get_ss_connections.pl  1.12  10 years  redwards  only call if not in a ss
dp.pl  1.4  10 years  redwards  editing header info
rapid_propagation.pl  1.75  10 years  olson  use $num_neighbors internally instead of hardwired constant
pull_fasta_entries.pl  1.8  10 years  olson  do not attempt to remap incoming ids
compute_changed_ids_for_nrs.pl  1.5  10 years  olson  misc fixes
reduce_sims.pl  1.12  10 years  olson  fix nasty little bug that drops sims
sequence_dereplication.pl  1.1  10 years  arodri7  first version of sequence_dereplication. Script takes sequences which are subset...
gd_tree.pl  1.1  10 years  golsen  Add a command line program to make a png graphic from a newick tree file.
load_ec_names.pl  1.6  10 years  olson  support for change in format to the KEGG/ECtable.
fabric_vec.pl  1.1  10 years  overbeek  add ability to make fabric vecs
estimated_fabric.pl  1.1  10 years  overbeek  code for processing fabrics and population estimates
predicted_vs_actual.pl  1.1  10 years  overbeek  basic metagenomic tools
compute_PCA_for_metagenomes.pl  1.1  10 years  mkubal  called by PCA_ssav
compute_PCA_with_metagenomes_as_variables.pl  1.1  10 years  mkubal  called by PCA_mgav
pegs_in_subsystem.pl  1.6  10 years  overbeek  check for aux roles
get_pairs.pl  1.1  10 years  parrello  New script to find certain functional roles close together.
cache_comparison_data.pl  1.11  10 years  paczian  fixed load order of function files in RAST vs SEED organisms
make_peg_map_from_tbl.pl  1.3  10 years  olson  fix bug that made empty output
make_peg_maps_from_fasta.pl  1.2  10 years  olson  need to compute sims both directions because connections_between now uses bbhs.
check_for_new_genomes.pl  1.3  10 years  overbeek  print stats as you go
find_gaps.pl  1.9  10 years  gdpusch  Fixed (hopefully) incorrectly handled out-of-bounds cases.
backup_critical_data.pl  1.5  10 years  olson  fix bug that kept subsystems from being backedup
compute_genome_counts.pl  1.25  10 years  olson  Fix bug where compute_genome_counts fails to run on a genome directory with mult...
extract_DNA_for_whole_ORFs.pl  1.4  10 years  gdpusch  Fixed possible DNA case sensitivity.
reformat_circular_contigs.pl  1.1  10 years  arodri7  added reformat_circular_contigs for rapid_propagation_plasmids
run_gene_calling_scripts.pl  1.3  10 years  overbeek  fix first arg on call to mark_picked_genes
mark_picked_genes.pl  1.2  10 years  overbeek  fix order of arguments
compare_two_sets_of_calls.pl  1.3  10 years  overbeek  stuff for gene calling
generate_comparisons.pl  1.1  10 years  overbeek  stuff for gene calling
generate_picked.pl  1.1  10 years  overbeek  stuff for gene calling
assign_figfam.pl  1.1  10 years  arodri7  add original assign_using_ff
get_rna_features_for_calling_genes.pl  1.2  10 years  overbeek  get rid of proteins
assign_using_ff_original.pl  1.1  10 years  arodri7  original format of assign_using_ff
gff2seed.pl  1.29  10 years  redwards  removing check for refseq ids
pick_feature_set.pl  1.1  10 years  overbeek  choose genes from candidates
merge_assignments.pl  1.1  10 years  bartels  *** empty log message ***
get_FIGfams_SS_NMPDR_stats.pl  1.1  10 years  arodri7  *** empty log message ***
assign_using_ff_parallel.pl  1.2  10 years  arodri7  made updates to functions used for updating FIGfams
fasta_size.pl  1.1  10 years  overbeek  add fasta_size
update_SSU_rRNAs.pl  1.1  10 years  overbeek  update of SSUs
convert-blast-to-m8.pl  1.1  10 years  olson  Convert full blast output to -m8 output using Gary's blast parsing code.
aclh_reload_contrib.pl  1.2  10 years  wilke  added db handle in ach call
make_partition_repsW.pl  1.1  10 years  overbeek  try
make_partition_reps.pl  1.1  10 years  overbeek  try
format_partition_dbs.pl  1.2  10 years  overbeek  try
make_sims_and_fc_data.pl  1.1  10 years  overbeek  add wrapper to building partition-based similarity and fc data
make_initial_partition_scores.pl  1.1  10 years  overbeek  additions to support partitioning of sims
index_translations_MD5.pl  1.4  10 years  olson  revert changes
WebAppBackend.pl  1.2  10 years  jared  make user and org commands case insensitive
index_sims.pl  1.12  10 years  olson  Bump id size.
make_sim_part_data.pl  1.1  10 years  overbeek  add command to build similarity partitions
connections_between.pl  1.8  10 years  overbeek  fixes to making close strain data
make_close_strain_data.pl  1.14  10 years  overbeek  fixes to making close strain data
difference_between_two_databases.pl  1.1  10 years  redwards  code for generating the delta between two databases
sims_all.pl  1.6  10 years  overbeek  remove paralogs before computing conections
check_all_subsystems.pl  1.11  10 years  olson  Transform the single big select into a prepared statement on per-role select.s
load_ss_classification.pl  1.1  10 years  redwards  adding ss classification methods
dump_ss_classification.pl  1.1  10 years  redwards  adding ss classification methods
assess_completeness.pl  1.9  11 years  gdpusch  Fixed leading-whitspace bug.
make_md5_figfams_file.pl  1.1  11 years  arodri7  script makes the md5 to figfams file
check_model_v2.pl  1.2  11 years  dejongh  switch to scenario_directory
make_model_spreadsheets.pl  1.2  11 years  dejongh  switch to scenario_directory
run_flux_optimization.pl  1.4  11 years  dejongh  switch to scenario_directory
find_missing_lib_inputs.pl  1.6  11 years  dejongh  switch to scenario_directory
find_missing_lib_inputs_v2.pl  1.2  11 years  dejongh  switch to scenario_directory
run_model_generation.pl  1.17  11 years  dejongh  switch to scenario_directory
find_essential_reactions.pl  1.3  11 years  dejongh  switch to scenario_directory
make_SBML_model.pl  1.6  11 years  dejongh  switch to scenario_directory
find_model_information.pl  1.7  11 years  dejongh  switch to scenario_directory
check_for_scenario_reachability.pl  1.3  11 years  dejongh  switch to scenario_directory
find_model_cofactors.pl  1.7  11 years  dejongh  switch to scenario_directory
make_MFA_tool_input.pl  1.2  11 years  dejongh  switch to scenario_directory
make_MPS_model.pl  1.7  11 years  dejongh  switch to scenario_directory
find_model_information_v2.pl  1.2  11 years  dejongh  switch to scenario_directory
run_scenarios.pl  1.5  11 years  dejongh  switch to scenario_directory
make_MPS_model_v2.pl  1.2  11 years  dejongh  switch to scenario_directory
run_model_generation_v3.pl  1.3  11 years  dejongh  switch to scenario_directory
check_model.pl  1.7  11 years  dejongh  switch to scenario_directory
compare_scenarios.pl  1.5  11 years  dejongh  Changes to move the 'All' scenarios directory to FIG_Config::global/Models/All
analyze_scenario_connections.pl  1.4  11 years  dejongh  Changes to move the 'All' scenarios directory to FIG_Config::global/Models/All
load_links.pl  1.7  11 years  olson  Only load links from files ending in "links" (rather than files with it anywhere...
Tracer.pl  1.1  11 years  parrello  New script used to route STDERR messages to the trace log.
WikiMaker.pl  1.6  11 years  parrello  Added more trace messages.
make_subsys_based_families.pl  1.14  11 years  overbeek  do not use genomes with variants beginning with an asterisk in forming FIGfams b...
function_of.pl  1.5  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
functionally_coupled.pl  1.7  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
get_ev_codes.pl  1.15  11 years  parrello  Updated comments to mention the replacement scripts.
ev_code_cron.pl  1.16  11 years  parrello  Updated comments to mention the replacement scripts.
ListLits.pl  1.1  11 years  parrello  New script to count literature references for NMPDR.
make_assertions_from_uploads.pl  1.3  11 years  overbeek  get rid of debugging message
assign_to_unchanged.pl  1.3  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
fig_net.pl  1.4  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
generate_similarities.pl  1.3  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
fig_rpc.pl  1.4  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
get_id_mapping_for_list_of_IDs.pl  1.1  11 years  wilke  Draft version for id mapping
set_not_private.pl  1.1  11 years  bartels  *** empty log message ***
find_special_proteins.pl  1.4  11 years  gdpusch  Suppress writing "called_by" and "special_pegs" when "-keep" is selected. -- /gd...
auto_assign.pl  1.19  11 years  olson  Add -orgdir option to use FIGV and its indexed sims.
load_dlits.pl  1.5  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
export_dlits.pl  1.2  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
compute_extra_dlit_data.pl  1.4  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
to_structured_english.pl  1.1  11 years  overbeek  add routine to build structured english rendering of evidence codes
get_synonyms_from_ach_for_id.pl  1.2  11 years  wilke  *** empty log message ***
seed2gff.pl  1.36  11 years  redwards  getting rid of need for strain info
generate_dlit_ev_codes.pl  1.5  11 years  overbeek  switching to new ilidt/dlit stuff
generate_ilit_ev_codes.pl  1.4  11 years  overbeek  code relating to dlit/ilit maintenance
uni_lit_to_dlits.pl  1.1  11 years  overbeek  dlit support
add_structured_english.pl  1.4  11 years  disz  Added escape arg to structured engkish
connect_PDB_to_FIGfams.pl  1.1  11 years  arodri7  update changes
connect_PDB_to_FIGfams_worker.pl  1.1  11 years  arodri7  update changes
figfam_size_distribution.pl  1.1  11 years  arodri7  update changes
test_figfam_peg.pl  1.6  11 years  arodri7  update changes
map_to_scaffold.pl  1.4  11 years  olson  Actually write out the changed entries.
make_Ontology_database.pl  1.3  11 years  mkubal  provides usage when no argument given
make_pfam_ontology.pl  1.4  11 years  mkubal  provides usage when no argument given
make_prosite_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_cdd_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_interpro_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_pdb_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_pir_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_go_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
gff2ncbitab.pl  1.3  11 years  olson  add swissprot
show_structured_english.pl  1.1  11 years  disz  Ross's code to generate annotations for NCBI
TestLocations.pl  1.8  11 years  parrello  Converted to use new name for Contrain method.
load_features.pl  1.24  11 years  olson  fix tmp file name.
index-pegsyn2.pl  1.1  11 years  olson  new version of pegsyn indexer that presorts data before inserting into the btree...
compute_ev_code_attributes.pl  1.2  11 years  overbeek  do not include cluster-based subsystems in forming evidence codes
crc64.py  1.1  11 years  mkubal  uses for mapping of interpro downlaod to pegs
index_feature_dir_fasta.pl  1.1  11 years  olson  Index scripts for FIGV accleration.
index_figv_annos.pl  1.1  11 years  olson  Index scripts for FIGV accleration.
trace.pl  1.3  11 years  parrello  Fixed so that the destination is not case-sensitive.
build_partition_index.pl  1.1  11 years  overbeek  return empty list of failure to open FIFfam
make_trimmed_alignment_from_ids.pl  1.13  11 years  overbeek  return empty list of failure to open FIFfam
test_figfam_FF_peg.pl  1.3  11 years  olson  Missed one of the figfamdata fixes.
install_anticipated_functions.pl  1.3  11 years  olson  Introduct &FIG::get_figfams_data()
check_figfams.pl  1.6  11 years  olson  Introduct &FIG::get_figfams_data()
load_ACH_resolution_DB.pl  1.4  11 years  overbeek  fixes to quotemeta characters in loading comments
export_ACH_resolution_DB.pl  1.2  11 years  overbeek  fixes relating to comments
map-nr-ids-to-ncbi-std.pl  1.1  11 years  olson  Script to map IDs in a SEED NR into forms acceptable to the indexed NCBI fasta p...
SpanishInquisition.pl  1.1  11 years  parrello  Added for testing the Confess method.
summarize_taxonomy_by_blast.pl  1.9  11 years  redwards  removing fatal error if 0 or 1 hits
get_NCBI_genome_attributes.pl  1.1  11 years  arodri7  get_NCBI_genome_attributes searches the NCBI internet sites for genome attribute...
load_id_correspondence.pl  1.3  11 years  olson  updates to the load_id_correspondence loader and searching code.
install_features_batch.pl  1.1  11 years  olson  Add new script to install a batch of genomid.tbl / genomeid.fasta files. Initial...
Consistency_Families.pm  1.1  11 years  bartels  *** empty log message ***
recompute_comparison.pl  1.1  11 years  bartels  *** empty log message ***
createTIGRfamSrc.pl  1.1  11 years  bartels  *** empty log message ***
make_tf_equivalog_file.pl  1.1  11 years  bartels  *** empty log message ***
check_subs_and_split_warnings.pl  1.3  11 years  overbeek  minor fix to handle deleted subsystems
build_anno_clearinghouse.pl  1.6  11 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
build_nr.pl  1.22  11 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
find_neighbors_by_sim.pl  1.4  11 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
compute_pins.pl  1.4  11 years  olson  undo bogus commit
load_bbhs.pl  1.15  11 years  olson  *** empty log message ***
expand_sims.pl  1.2  11 years  olson  *** empty log message ***
fast_blastp.pl  1.1  11 years  overbeek  fast_blastp is a tool to support rapid similarity estimates using FIGfam partiti...
TransactFeatures.pl  1.20  11 years  parrello  Removed obsolete use clause.
PickGeneBoundariesTest.pl  1.1  11 years  parrello  Test script for backfill.
OneShotAttributeAdder.pl  1.2  11 years  parrello  Removed obsolete use clauses.
NMPDRAnalysis.pl  1.5  11 years  parrello  Removed obsolete use clauses.
LigandCleanup.pl  1.2  11 years  parrello  Removed obsolete use clases.
import_similarity_bundle.pl  1.3  11 years  parrello  Fixed a POD error.
exclude_genomes.pl  1.3  11 years  parrello  Fixed a POD error.
backup_subsystems.pl  1.3  11 years  parrello  Fixed a POD error.
aclh.pl  1.11  11 years  paarmann  added new parameter to dump contribs
subsys_info.pl  1.1  11 years  overbeek  subsys_info is subsystem information for Verionika
find_subsys.pl  1.3  11 years  overbeek  allow loose matching in rapid_propagation
prepare_metagenome_files_for_download.pl  1.4  11 years  mkubal  full loop
mg_user_id_to_unique.pl  1.2  11 years  mkubal  full loop
metagenome2genbank.pl  1.4  11 years  mkubal  includes data from meta.xml
make_uniprot_corr.pl  1.2  11 years  overbeek  build uniprot correspondence
build_initial_objects_for_start_predictions.pl  1.12  11 years  gdpusch  Modified to also work on new genomes using "FIGV.". -- /gdp
get_dna.pl  1.6  11 years  gdpusch  Minor cosmetic change. -- /gdp
prepare_metagenome_files_for_ftp.pl  1.3  11 years  mkubal  checks for PUBLIC file
run_remote_Phobius_for_fasta.pl  1.1  11 years  mkubal  fasta file as input
update_lineage.pl  1.3  11 years  wilke  draft version to update FIG taxonomy entries
adjacent.pl  1.3  11 years  redwards  changing chop to chomp
correct_gff_missing_contigs.pl  1.5  11 years  redwards  correcting a weird error
Packager.pl  1.7  11 years  parrello  Changed POD format for better compatability with Wiki.
find_selenoproteins.pl  1.4  11 years  golsen  Add functions to reference selenoproteins, and add change the set slightly. Rep...
Makefile.cprogs  1.2  11 years  olson  Support compilation of nap.c
add_rbs_data_for_start_predictions.pl  1.3  11 years  gdpusch  Added FIGV support. -- /gdp
order_corrections_for_start_predictions.pl  1.5  11 years  gdpusch  Added FIGV support. -- /gdp
add_sim_data_for_start_predictions.pl  1.8  11 years  gdpusch  Added FIGV support. -- /gdp
get_sims_for_start_predictions.pl  1.5  11 years  gdpusch  Added FIGV support. -- /gdp
predict_starts.pl  1.8  11 years  gdpusch  Added FIGV support. -- /gdp
start_data_for_set_of_pegs.pl  1.6  11 years  gdpusch  Added FIGV support. -- /gdp
add_start_data_for_start_predictions.pl  1.4  11 years  gdpusch  Added FIGV support. -- /gdp
get_potential_starts_for_start_predictions.pl  1.3  11 years  gdpusch  Added FIGV support. -- /gdp
make_calls_for_start_predictions.pl  1.4  11 years  gdpusch  Added FIGV support. -- /gdp
install-data.pl  1.8  11 years  olson  fix to dvd data installer
find_poss_fs.pl  1.1  11 years  overbeek  add code to fix frameshifts in a genome
test_placement.pl  1.1  12 years  overbeek  redone FIGfam stuff
check_peg_placement.pl  1.1  12 years  overbeek  redone FIGfam stuff
index_anno_clearinghouse.pl  1.3  12 years  olson  multiple id support, build fixes
install_rast_batch.pl  1.4  12 years  olson  more fixes
genome_peg_dna.pl  1.3  12 years  golsen  Extensive modifications to allow more options, and handle large genomes by not r...
get_evaluation_check_rast_new_vs_old.pl  1.1  12 years  bartels   compare old rast with development version
fix_invalid_fasta.pl  1.1  12 years  redwards  Initial release of programs to check and fix valid fasta format
validate_fasta.pl  1.1  12 years  redwards  Initial release of programs to check and fix valid fasta format
run_find_subsys_against_all_genomes.pl  1.2  12 years  overbeek  updates to computation of VCs
install_new_coupling_data.pl  1.3  12 years  olson  add option to install from a jobdir
add_figbar_and_genome_attributes.pl  1.1  12 years  mkubal  v1
parse_uniparc.pl  1.1  12 years  mkubal  v1
compute_crc64_for_all_pegs.pl  1.1  12 years  mkubal  v1
features_with_role.pl  1.1  12 years  golsen  Function to get the ids or sequences of features that match a given role. Uses F...
get_subsystem_properties.pl  1.1  12 years  overbeek  minor modifications to get subsystems statistics
index_annotations.pl  1.11  12 years  olson  bugfix
check_for_possible_mobile_elements.pl  1.1  12 years  overbeek  add code to search for mobile elements
sort_and_split_bbhs.pl  1.5  12 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
all_bbhs.pl  1.16  12 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
make_reduce_sims_index.pl  1.1  12 years  olson  new script
flip_sims.pl  1.7  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
reformat_sims.pl  1.8  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
reformat_timelogic_sims.pl  1.2  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
run_remote_Phobius_for_genomes.pl  1.1  12 years  mkubal  run for all complete prok genomes
run_remote_Phobius_for_genome_for_RAST.pl  1.1  12 years  mkubal  for use with RAST server
close_connections.pl  1.2  12 years  overbeek  add strip comments argument on function_of
merge_families.pl  1.3  12 years  overbeek  add strip comments argument on function_of
ali_tree.pl  1.4  12 years  overbeek  add strip comments argument on function_of
sims_between.pl  1.7  12 years  overbeek  updates on close connections
run_remote_Phobius_for_genome.pl  1.1  12 years  mkubal  for single genome
make_PFAM_HMM_derived_attributes.pl  1.2  12 years  mkubal  added date as 2nd argument
make_Phobius_attributes.pl  1.2  12 years  mkubal  added date as 2nd argument
run_remote_PHOBIOUS.pl  1.1  12 years  mkubal  runs Phobius computation for given geneome
run_HMM_search_on_timelogic.pl  1.1  12 years  mkubal  version 1.0
get_evaluation_check.pl  1.3  12 years  bartels  added option -a for showing pegs that do not match via blast
rebuild_global_chromosomal_clusters.pl  1.2  12 years  overbeek  version of rebuild_global_chromosomal_clusters that works
same_figfam.pl  1.2  12 years  overbeek  handle bad input in same_figfam
run_model_generation_all.pl  1.1  12 years  formsma  This script will generate models for all complete genomes in the seed. - Kevin
compute_mw_and_pi_with_BioPerl.pl  1.1  12 years  mkubal  computes mw and pi for all pegs in complete genomes
make_fasta_btree.pl  1.1  12 years  olson  Utility for creating btree access for fasta files.
predict_scenarios.pl  1.2  12 years  formsma  Added code to automatically run 'run_scenarios All' if it hasn't been run. These...
trim_alignment.pl  1.2  12 years  overbeek  minor fixes
update-caches.pl  1.1  12 years  olson  Update SEED caches.
make_sp_uni_files.pl  1.4  12 years  wilke  changed check for input and output directory the directories may exists, so don'...
test_Observation.pl  1.1  12 years  mkubal  for testing
compute_pchs_from_sims.pl  1.2  12 years  olson  Rollup of changes for the new RAST install.
remove_clustered_pchs2.pl  1.1  12 years  olson  Missing scripts.
remove_sims_not_in_nr.pl  1.1  12 years  olson  Missing scripts.
maint-remove-obsolete-aliases.pl  1.1  12 years  olson  Missing scripts.
remove_clustered_pchs3.pl  1.1  12 years  olson  Missing scripts.
compute_genome_similarity.pl  1.1  12 years  olson  Missing scripts.
register_genome_with_clearinghouse.pl  1.1  12 years  olson  Missing scripts.
index-pegsyn.pl  1.1  12 years  olson  Missing scripts.
check_fasta_for_dups.pl  1.1  12 years  olson  Missing scripts.
make_ncbi_files.pl  1.4  12 years  wilke  changed check for existing directories
gff2tab.pl  1.5  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
build_figfam_pssm_db.pl  1.2  12 years  gdpusch  Major modifications to &load_family_ids()
reps_and_close.pl  1.2  12 years  overbeek  add make_trimmed_alignment_from_ids
align_seqs.pl  1.1  12 years  overbeek  add utilities for computing alignments
order_seqs_on_length.pl  1.1  12 years  overbeek  add utilities for computing alignments
build_nr_sources.pl  1.14  12 years  olson  Rollup of various rast-related changes.
process_new_sims.pl  1.6  12 years  olson  Rollup of various rast-related changes.
collect_related_sequences.pl  1.3  12 years  golsen  Encapsulate all of the SEED-dependent functions in the perl module. It should st...
split_and_trim_sequences.pl  1.14  12 years  overbeek  fix problem when repeats occur
runclustalw.pl  1.4  12 years  overbeek  add computation of alignments to building FIGFAMS
filter_figfams.pl  1.2  12 years  overbeek  add computation of alignments to building FIGFAMS
run_glimmer2.pl  1.7  12 years  gdpusch  Added support for multiple genetic codes. -- /gdp
best_tree_using_proml_on_cluster.pl  1.1  12 years  overbeek  add best_tree_using_proml_on_cluster
bayes_expected_start_scores.pl  1.3  12 years  overbeek  Added comments to expalin logic. -- gdp
index_nr.pl  1.2  12 years  olson  compute length btree also
compute_contig_md5.pl  1.4  12 years  olson  rollup of metagenome server changes
align_with_clustal_2.pl  1.4  12 years  golsen  Trivial format change.
make_CDD_attributes.pl  1.2  12 years  mkubal  fix to score format
make_PDB_attributes.pl  1.2  12 years  mkubal  fix to score format
make_PROSITE_PIR_PRODOM_attributes.pl  1.3  12 years  mkubal  fix to score format
make_IPR_PFAM_GO_attributes.pl  1.3  12 years  mkubal  fix to score format
load_close.pl  1.9  12 years  overbeek  tighten length constraints for figfam matching
direct_functional_coupling.pl  1.4  12 years  overbeek  tighten length constraints for figfam matching
make_sim_tab.pl  1.8  12 years  olson  compute_pchs_from_sims.pl
subsys2pubmed.pl  1.4  12 years  hwang  change script to add new attribute after each subsystem versus after all subsyst...
get_taxid_journals.pl  1.1  12 years  hwang  get journals from PMC using taxide
get_journals_for_org.pl  1.1  12 years  hwang  this script is the backend to get journals using taxonomy id or name. This calls...
get_pubmed_journals.pl  1.5  12 years  hwang  update comment that this is for peg curation
ensure_genome_registration.pl  1.1  12 years  olson  generate feature registration stuff
explore_subsys_pmid.pl  1.5  12 years  hwang  PEG information is no longer stored in the file. Parsing of the file in this scr...
compareMR.pl  1.1  12 years  overbeek  basic stuff for comparing metabolic reconstructions
possible_frameshifts.pl  1.1  12 years  overbeek  update possible_frameshifts
update_uniq_id_data.pl  1.7  12 years  olson  use function_of_quick
get_journals_for_frole.pl  1.1  12 years  hwang  Files to get journal information from PubMed
submit_genome_to_rpsblast_against_CDD_on_biocluster.pl  1.2  12 years  mkubal  test for dir exist
submit_genome_to_signalP.pl  1.2  12 years  mkubal  test for dir exist
compute_CELLO_and_TMPRED.pl  1.2  12 years  mkubal  test for dir exist
compute_mw_and_pi.pl  1.2  12 years  mkubal  one genome at a time
submit_to_iprscan_on_biocluster.pl  1.1  12 years  mkubal  run iprscan on cluster
make_CELLO_and_TMPRED_attributes.pl  1.2  12 years  mkubal  changed ; to :: for key separator
make_SignalP_attributes.pl  1.2  12 years  mkubal  changed ; to :: for key separator
blast_pdb_against_nr_on_tla.pl  1.1  12 years  mkubal  blast pdb against nr
trimmed_kernel_alignment.pl  1.1  12 years  overbeek  add last round of phylogeny tools
add_prots_to_tree.pl  1.1  12 years  golsen  New script for adding proteins to an existing tree.
add_attributes_from_file.pl  1.1  12 years  redwards  just a simple attribute loader
blastn_chunks.pl  1.3  12 years  overbeek  initial, undebugged version of edit_feature.cgi
make_proml_tree.pl  1.6  12 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
make_proml_tree_0.pl  1.1  12 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
check_subsystems.pl  1.7  12 years  overbeek  strip comments on functions for subsystem checking
insert_prot_into_tree.pl  1.14  12 years  golsen  Continuing the update of tree packages and programs
bring_tree_up_to_ali.pl  1.5  12 years  overbeek  debugged version of bring_tree_up_to_ali
make_neigh_joining_tree.pl  1.8  12 years  overbeek  debugged version of bring_tree_up_to_ali
evaluate_quality_of_trees.pl  1.4  12 years  overbeek  debugged version of bring_tree_up_to_ali
make_protein_weights_and_rates.pl  1.2  12 years  golsen  Moving some tree building tools into packages.
to_arabidopsis.pl  1.1  12 years  hwang  This script parses arabidopsis.org to get the AT aliases output
make_kegg_files.pl  1.5  12 years  overbeek  Update parsing of NAME field to reflect change in source file. -- /gdp
make_parallel_proml_run.pl  1.2  12 years  overbeek  add rates to phylogeny stuff
insert_into_a_tree.pl  1.5  12 years  overbeek  add tree_neighbors and latest phylogeny stuff
uproot.pl  1.1  12 years  overbeek  add uproot
tips_of.pl  1.3  12 years  overbeek  add insert_prot_into_tree, a new way to insert proteins into a tree
check_and_extend_all_subsystems.pl  1.7  12 years  overbeek  fix call to rapid_subsystem_extension in check_and_extend_all_subsystems
remove_clustered_pchs.pl  1.10  12 years  overbeek  fix rfemove_clustered_PCHs to count correctly
gff_statistics.pl  1.1  12 years  redwards  releasing gff statistics
rep_genomes.pl  1.1  12 years  overbeek  fixes to representative tree generation and added rep_genomes
generate_GO_attributes.pl  1.1  12 years  overbeek  add GO attribute genertation
load_go.pl  1.2  12 years  overbeek  put in the fr2go stuff
update_fr2go.pl  1.1  12 years  overbeek  put in the fr2go stuff
make_external_sequence_data.pl  1.2  12 years  olson  remove .pl from invocations
make_timestamps.pl  1.4  12 years  overbeek  add initial version of FIGO.pm - OO services
extract_sp_links.pl  1.3  13 years  olson  fix -h error
compare_tbls.pl  1.5  13 years  overbeek  Minor change to output. -- /gdp
indirect_functional_coupling.pl  1.5  13 years  overbeek  indirect functional coupling should not be from a PEG to itself
indirect_functional_coupling_mcauliffe.pl  1.5  13 years  overbeek  indirect functional coupling should not be from a PEG to itself
filter_overlaps.pl  1.5  13 years  overbeek  Added some more diagnosting lines. -- /gdp
genomes_with_essentiality_data.pl  1.1  13 years  redwards  Adding tools to handle essentiality data for Sveta
seed_run_job.pl  1.4  13 years  olson  readonly fixes; seed-run-job update to run from input file
seed_run_task.pl  1.2  13 years  olson  readonly fixes; seed-run-job update to run from input file
score_dfcs_mcauliffe.pl  1.5  13 years  overbeek  limit decimal positions in score
split_by_genome.pl  1.1  13 years  overbeek  split_by_genome can be used to split a score or BBH file
load_locks.pl  1.1  13 years  overbeek  introduce locks on features to block assignments
bielefeld_tarfile_to_seed.pl  1.7  13 years  overbeek  Tweaked usage msg. -- /gdp
track_figfams.pl  1.2  13 years  overbeek  get rid of diagnostics in track_figfams
check_sims_basic.pl  1.8  13 years  redwards  using is_environmental instead of seven 9s
fig_specific_sequences.pl  1.3  13 years  redwards  using is_environmental instead of seven 9s
extend_subsys.pl  1.7  13 years  redwards  using is_environmental instead of seven 9s
pubmed_gene2peg.pl  1.2  13 years  redwards  making sure gene id is right
build_alignments_from_spreadsheet.pl  1.7  13 years  redwards  using is_environmental
add_to_subsystems.pl  1.1  13 years  overbeek  add add_to_subsystems
potentially_missed_assignments.pl  1.1  13 years  overbeek  add potentially_missed_assignments
iedb.pl  1.10  13 years  overbeek  RAE: bugger, correcting the array dereferencing
get_figfam_funcs.pl  1.1  13 years  overbeek  add install_anticipated_functions and some FIGfam tracking stuff
peg2pubmed.pl  1.1  13 years  hwang  Added two scripts that will generate pubmed files
score_ifcs_mcauliffe.pl  1.2  13 years  overbeek  RAE: correcting indirect functional coupling score
to_org_specific.pl  1.4  13 years  hwang  fix syntax error
score_ifcs.pl  1.4  13 years  overbeek  RAE: More direct and indirect functional coupling scores
score_dfcs.pl  1.3  13 years  overbeek  RAE: removing the header that should not be in the source
make_figfams.pl  1.3  13 years  overbeek  families.2c should get current function - not family function
make_close.pl  1.7  13 years  parrello  Fixed obsolete form of boundaries_of.
map_pegs.pl  1.3  13 years  parrello  Fixed obsolete form of boundaries_of.
make_FigFamsData.pl  1.4  13 years  overbeek  order generated FIGfams
order_figfams.pl  1.1  13 years  overbeek  order_figfams
make_close_strain_family_tabs.pl  1.2  13 years  overbeek  fixes to wseekly statistics
find_bad_conflicts.pl  1.1  13 years  overbeek  fixes to wseekly statistics
make_proposed_assignments_for_consistency.pl  1.4  13 years  overbeek  fixes to wseekly statistics
load_pirsf.pl  1.14  13 years  overbeek  RAE: correcting load_pirsf not recognizing a firewall
index_pins.pl  1.3  13 years  olson  new pin indexer
seed2pir.pl  1.3  13 years  overbeek  RAE: moving PIRSF to links
filter_tbl_overlaps.pl  1.10  13 years  overbeek  set up find_neighbors to handle existing genomes
read_write_excel.pl  1.1  13 years  overbeek  RAE: Initial release of a simple script to read and write excel files to allow e...
new_versions_of_features.pl  1.1  13 years  overbeek  add new_versions_of_features
extract_fasta_idmap.pl  1.1  13 years  overbeek  RAE: Adding FigKernelScripts/extract_fasta_idmap.pl
assign_to_close_strains.pl  1.10  13 years  overbeek  fixes to Assignments.pm
get_translations.pl  1.3  13 years  overbeek  get_translations can take PEG ids from STDIN
myjoin.pl  1.1  13 years  overbeek  fix building FigFamData
split_clean_unclean_families.pl  1.4  13 years  overbeek  fixes for splitting families into clean/unclean
split_assignments_based_on_subsystems.pl  1.1  13 years  overbeek  next version of the STAG code
delete_all_attribute_files.pl  1.2  13 years  overbeek  RAE: New delete attribute files to remove all files. maybe this will work
purge_fasta.pl  1.1  13 years  overbeek  Removes duplicate entries from fasta file. -- /gdp
purge_tbl.pl  1.1  13 years  overbeek  Removes duplicate entries from tbl file. -- /gdp
load_coupling.pl  1.9  13 years  olson  Remove debugging.
load_sims.pl  1.10  13 years  olson  If we are loading unmapped files (as generated by make_close -no-map and make_s...
export_similarity_request.pl  1.3  13 years  overbeek  minor fixes to assignment for close strains
curator_of.pl  1.1  13 years  overbeek  minor fixes to assignment for close strains
nmpdr2gff.pl  1.1  13 years  overbeek  RAE: Changes to gff3 files for NMPDR and adding nmpdr2gff for creating the files...
salvage_annotations.pl  1.6  13 years  olson  bugfix.
update_nr_cycle.pl  1.6  13 years  overbeek  load ext org table on update_nr_cycle
compute_sim_chunk.pl  1.3  13 years  olson  add working-on-chunk support
extract_genomes.pl  1.38  13 years  overbeek  changes to support dynamic sims and updates
boot_cluster_seed.pl  1.5  13 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
compute_dbdir_checksum.pl  1.3  13 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
compute_potential_fusions.pl  1.12  13 years  overbeek  fix to fusions
salvage_subsystem_rows.pl  1.6  13 years  overbeek  fixes to salvage code
salvage_master_annotations.pl  1.3  13 years  overbeek  fixes to salvage code
initialize_alignments_for_subsystems.pl  1.2  13 years  overbeek  fixes to extract_genomes, salvage_subsystem_rows and initialize_alignments_for_s...
index_contig_files.c  1.5  13 years  olson  fix to work on 64-bit linux
flattened_to_fasta.pl  1.1  13 years  overbeek  add some minor utilities to flatten/unflatten fasta files
flatten_fasta.pl  1.1  13 years  overbeek  add some minor utilities to flatten/unflatten fasta files
same_subsys.pl  1.1  13 years  overbeek  fixes to extract_genomes
are_close.pl  1.1  13 years  overbeek  fixes to extract_genomes
load_abstract_coupling.pl  1.3  13 years  parrello  Changed to use a single-character delimiter (for compatability with PostGRES).
make_fam_tabs.pl  1.5  13 years  overbeek  RAE: Protein Families interface and construction
create_sims_btree.pl  1.1  13 years  olson  BTREE-index versions of these. Experimental still.
load_coupling_btree.pl  1.1  13 years  olson  BTREE-index versions of these. Experimental still.
load_bbhs_btree.pl  1.1  13 years  olson  BTREE-index versions of these. Experimental still.
load_protein_families.pl  1.9  13 years  overbeek  RAE: extending protein families
make_peg_maps.pl  1.3  13 years  overbeek  minor fixes
Simple.pl  1.4  13 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
test_parse_gff.pl  1.3  13 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
sync_new_system.pl  1.6  13 years  golsen  Just adding a newline at end of file to make repository match my working copy. ...
COPYING.TXT  1.1  13 years  olson  add license file
md5.c  1.3  13 years  olson  Doh, put proper comments in for C code.
fasta_cksum.c  1.4  13 years  olson  Doh, put proper comments in for C code.
fastasize.c  1.3  13 years  olson  Doh, put proper comments in for C code.
run_start_predictions_for_all_subsystems.pl  1.4  13 years  olson  Add license words.
relevant_pchsG.pl  1.4  13 years  olson  Add license words.
update_sims.pl  1.13  13 years  olson  Add license words.
show_reconfig_cmd.pl  1.3  13 years  olson  Add license words.
split_sims.pl  1.3  13 years  olson  Add license words.
sp2fasta.pl  1.2  13 years  olson  Add license words.
register_features_with_clearinghouse.pl  1.2  13 years  olson  Add license words.
run_start_predictions_for_spreadsheet.pl  1.6  13 years  olson  Add license words.
sprout_search.pl  1.2  13 years  olson  Add license words.
split_and_install_pchs.pl  1.2  13 years  olson  Add license words.
questionable_calls.pl  1.2  13 years  olson  Add license words.
select_genomes_for_sprout.pl  1.2  13 years  olson  Add license words.
synchronize_annotations_and_assignments.pl  1.2  13 years  olson  Add license words.
verify_pegs_in_tbl.pl  1.2  13 years  olson  Add license words.
test_cv.pl  1.2  13 years  olson  Add license words.
validate_subsystem.pl  1.2  13 years  olson  Add license words.
validate_genome_gff.pl  1.6  13 years  olson  Add license words.
run_fc.pl  1.2  13 years  olson  Add license words.
test_generate_anno_gff.pl  1.3  13 years  olson  Add license words.
relabel_nodes.pl  1.2  13 years  olson  Add license words.
stop_services.pl  1.5  13 years  olson  Add license words.
process_sim_deletions_and_replacements.pl  1.3  13 years  olson  Add license words.
restrict_by_similarity.pl  1.4  13 years  olson  Add license words.
similar_to.pl  1.4  13 years  olson  Add license words.
upstream.pl  1.3  13 years  olson  Add license words.
root_at.pl  1.2  13 years  olson  Add license words.
project.pl  1.2  13 years  olson  Add license words.
roles_in_subsystem.pl  1.2  13 years  olson  Add license words.
to_map_coords.pl  1.3  13 years  olson  Add license words.
run_peg_job_worker.pl  1.4  13 years  olson  Add license words.
to_insert.pl  1.2  13 years  olson  Add license words.
where_does_seq_hit.pl  1.2  13 years  olson  Add license words.
set_to_relation.pl  1.2  13 years  olson  Add license words.
restore_annotations.pl  1.2  13 years  olson  Add license words.
pull_sp_entries.pl  1.2  13 years  olson  Add license words.
start_services.pl  1.12  13 years  olson  Add license words.
to_gg.pl  1.2  13 years  olson  Add license words.
restrict_to_genomes.pl  1.3  13 years  olson  Add license words.
translate.pl  1.2  13 years  olson  Add license words.
restore_assignments.pl  1.2  13 years  olson  Add license words.
reformat_dsim_dbs.pl  1.2  13 years  olson  Add license words.
to_gids.pl  1.2  13 years  olson  Add license words.
subtree_of.pl  1.2  13 years  olson  Add license words.
report_changes.pl  1.2  13 years  olson  Add license words.
translation_of.pl  1.2  13 years  olson  Add license words.
splitup.pl  1.4  13 years  olson  Add license words.
uninstall.pl  1.2  13 years  olson  Add license words.
register_features_batch.pl  1.2  13 years  olson  Add license words.
uninstall.sims.pl  1.2  13 years  olson  Add license words.
prep_viz.pl  1.2  13 years  olson  Add license words.
reformat_fasta.pl  1.2  13 years  olson  Add license words.
pp.pl  1.3  13 years  olson  Add license words.
put_directory_in_one_file.pl  1.2  13 years  olson  Add license words.
representative_tree.pl  1.2  13 years  olson  Add license words.
relevant_PCHs.pl  1.3  13 years  olson  Add license words.
restore_translation_rules.pl  1.2  13 years  olson  Add license words.
format_peg_dbs.pl  1.3  13 years  olson  Add license words.
index_sprout.pl  1.12  13 years  olson  Add license words.
export_subsystem_as_gff.pl  1.2  13 years  olson  Add license words.
compute_new_ids.pl  1.2  13 years  olson  Add license words.
build_nohit_fasta.pl  1.2  13 years  olson  Add license words.
count_bases.pl  1.2  13 years  olson  Add license words.
generate_Property_for_sprout.pl  1.6  13 years  olson  Add license words.
package_annotations.pl  1.9  13 years  olson  Add license words.
check_starts_for_pegs.pl  1.5  13 years  olson  Add license words.
fill_in_roles.pl  1.4  13 years  olson  Add license words.
is_prokaryotic.pl  1.2  13 years  olson  Add license words.
get_class_examples.pl  1.2  13 years  olson  Add license words.
install_assignments.pl  1.7  13 years  olson  Add license words.
make_subsystems_from_clusters.pl  1.5  13 years  olson  Add license words.
changed_starts.pl  1.7  13 years  olson  Add license words.
order_sets.pl  1.3  13 years  olson  Add license words.
assign_towards_subsystems.pl  1.2  13 years  olson  Add license words.
filter_pegs_in_subsystems.pl  1.4  13 years  olson  Add license words.
extract_data_for_syncing_after_update.pl  1.6  13 years  olson  Add license words.
clean_subsystems.pl  1.2  13 years  olson  Add license words.
dna_seq.pl  1.2  13 years  olson  Add license words.
complete_genomes.pl  1.7  13 years  olson  Add license words.
build_alignments_for_subsystems.pl  1.4  13 years  olson  Add license words.
load_external_orgs.pl  1.3  13 years  olson  Add license words.
check_lost_sims.pl  1.2  13 years  olson  Add license words.
init_peg_job_scheduler.pl  1.4  13 years  olson  Add license words.
make_attribute_index.pl  1.6  13 years  olson  Add license words.
get_nr_entries_without_sims.pl  1.4  13 years  olson  Add license words.
postprocess_computed_sims.pl  1.2  13 years  olson  Add license words.
generate_GenomeGroups_for_sprout.pl  1.3  13 years  olson  Add license words.
clustal2fasta.pl  1.2  13 years  olson  Add license words.
blastn_seqs.pl  1.2  13 years  olson  Add license words.
cluster_by_sim.pl  1.2  13 years  olson  Add license words.
bbhs.pl  1.7  13 years  olson  Add license words.
load_sets.pl  1.5  13 years  olson  Add license words.
compute_pins_and_clusters.pl  1.2  13 years  olson  Add license words.
db_xrefs_of.pl  1.4  13 years  olson  Add license words.
external_calls.pl  1.2  13 years  olson  Add license words.
gff2Ontology.pl  1.4  13 years  olson  Add license words.
compute_simple_scores.pl  1.4  13 years  olson  Add license words.
make_sp_func_syn_dicts.pl  1.2  13 years  olson  Add license words.
pegs_in_conflict.pl  1.3  13 years  olson  Add license words.
break_scaffolds.pl  1.2  13 years  olson  Add license words.
insert_all.pl  1.2  13 years  olson  Add license words.
check_alignment.pl  1.2  13 years  olson  Add license words.
apply_peg_changes_to_subsystem.pl  1.3  13 years  olson  Add license words.
load_pch_pins.pl  1.2  13 years  olson  Add license words.
gather_attributes.pl  1.8  13 years  olson  Add license words.
get_pathways_for_EC.pl  1.2  13 years  olson  Add license words.
fix_annotations.pl  1.2  13 years  olson  Add license words.
ali_to_seq.pl  1.2  13 years  olson  Add license words.
display_tree.pl  1.4  13 years  olson  Add license words.
make_transferable_tarfiles.pl  1.3  13 years  olson  Add license words.
all_subsystems.pl  1.2  13 years  olson  Add license words.
check_for_unique_sims.pl  1.2  13 years  olson  Add license words.
blast_request.pl  1.2  13 years  olson  Add license words.
location_of.pl  1.2  13 years  olson  Add license words.
cat_spreadsheet.pl  1.2  13 years  olson  Add license words.
make_match_table.pl  1.2  13 years  olson  Add license words.
aliases_of.pl  1.6  13 years  olson  Add license words.
make_PHOBs_for_subsystems.pl  1.5  13 years  olson  Add license words.
lengths_of_contigs.pl  1.2  13 years  olson  Add license words.
check_peg_assignments.pl  1.3  13 years  olson  Add license words.
embl2gff_addmd5.py  1.2  13 years  olson  Add license words.
make_assignments_set.pl  1.3  13 years  olson  Add license words.
initial_set.pl  1.2  13 years  olson  Add license words.
install_translation_rules.pl  1.3  13 years  olson  Add license words.
generate_pinned_homologs.pl  1.2  13 years  olson  Add license words.
apply_map.pl  1.2  13 years  olson  Add license words.
extract_DNA_sequence_from_object_for_start_predictions.pl  1.2  13 years  olson  Add license words.
alter_tbl.pl  1.4  13 years  olson  Add license words.
merge_translation_rules.pl  1.7  13 years  olson  Add license words.
extend_subsystem.pl  1.2  13 years  olson  Add license words.
map_sims.pl  1.5  13 years  olson  Add license words.
package_sims.pl  1.2  13 years  olson  Add license words.
fasta_to_phylip.pl  1.2  13 years  olson  Add license words.
install_lightweight_code.pl  1.2  13 years  olson  Add license words.
cluster_by_bbhs.pl  1.2  13 years  olson  Add license words.
assign_to_hypo.pl  1.3  13 years  olson  Add license words.
import_external_sequences_step3.pl  1.5  13 years  olson  Add license words.
alias2fig.pl  1.2  13 years  olson  Add license words.
assign_with_no_sims.pl  1.2  13 years  olson  Add license words.
is_archaeal.pl  1.2  13 years  olson  Add license words.
generate_Source_for_sprout.pl  1.2  13 years  olson  Add license words.
peg_to_pdb.py  1.2  13 years  olson  Add license words.
extract_genes.pl  1.5  13 years  olson  Add license words.
clean_sims.pl  1.2  13 years  olson  Add license words.
dump_machine_state.pl  1.3  13 years  olson  Add license words.
condense_blast.pl  1.2  13 years  olson  Add license words.
make_fig_files.pl  1.3  13 years  olson  Add license words.
assign_synonym_ids.pl  1.2  13 years  olson  Add license words.
generate_genome_feature_tables_for_sprout.pl  1.16  13 years  olson  Add license words.
get_empty_ecs.pl  1.4  13 years  olson  Add license words.
make_sprout_upstream.pl  1.2  13 years  olson  Add license words.
parse_mart.py  1.6  13 years  olson  Add license words.
load_distances.pl  1.5  13 years  olson  Add license words.
make_maps_from_sub.py  1.5  13 years  olson  Add license words.
keep_only.pl  1.2  13 years  olson  Add license words.
add_close_genes.pl  1.2  13 years  olson  Add license words.
map_sims_for_bigfc.pl  1.2  13 years  olson  Add license words.
make_sp_org_domain_table.pl  1.2  13 years  olson  Add license words.
get_empty_ecs  1.3  13 years  olson  Add license words.
expand_multifunctional_roles.pl  1.3  13 years  olson  Add license words.
load_hugo.pl  1.6  13 years  olson  Add license words.
fix_eol.pl  1.2  13 years  olson  Add license words.
peg_to_subsystems.pl  1.3  13 years  olson  Add license words.
package_translation_rules.pl  1.2  13 years  olson  Add license words.
generate_gene_blocks.pl  1.3  13 years  olson  Add license words.
make_phob_from_ids.pl  1.3  13 years  olson  Add license words.
init_dbserver.pl  1.3  13 years  olson  Add license words.
fill_in_cell.pl  1.2  13 years  olson  Add license words.
package_lightweight_code.pl  1.2  13 years  olson  Add license words.
genbank2gff3.pl  1.5  13 years  olson  Add license words.
paint_tree.pl  1.3  13 years  olson  Add license words.
make_sp_org_table.pl  1.2  13 years  olson  Add license words.
potentially_cotranscribed.pl  1.2  13 years  olson  Add license words.
p2p_sync_cron.pl  1.3  13 years  olson  Add license words.
possibly_truncated.pl  1.2  13 years  olson  Add license words.
fill_subsys.pl  1.5  13 years  olson  Add license words.
install_subsystems.pl  1.2  13 years  olson  Add license words.
delete_genomes_from_sims.pl  1.2  13 years  olson  Add license words.
match_dna_to_aligned_prots.pl  1.4  13 years  olson  Add license words.
export_genome_as_gff.pl  1.6  13 years  olson  Add license words.
compare_tree_and_alignment.pl  1.2  13 years  olson  Add license words.
check_nr_and_peg_synonyms.pl  1.2  13 years  olson  Add license words.
fid2dna.pl  1.2  13 years  olson  Add license words.
find_maximal_clusters.pl  1.2  13 years  olson  Add license words.
best_hits.pl  1.2  13 years  olson  Add license words.
fusion_of.pl  1.2  13 years  olson  Add license words.
html_parser.py  1.2  13 years  olson  Add license words.
interval.pl  1.2  13 years  olson  Add license words.
get_long_enough.pl  1.2  13 years  olson  Add license words.
make_sp_desc_with_org.pl  1.2  13 years  olson  Add license words.
check_fast_sims.pl  1.2  13 years  olson  Add license words.
install_annotations.pl  1.4  13 years  olson  Add license words.
das_test.pl  1.2  13 years  olson  Add license words.
install_feature_updates.pl  1.2  13 years  olson  Add license words.
check_all_lost_sims.pl  1.2  13 years  olson  Add license words.
is_eukaryotic.pl  1.2  13 years  olson  Add license words.
make_assignments_fit_initial_css.pl  1.4  13 years  olson  Add license words.
build_syn.pl  1.2  13 years  olson  Add license words.
extract_subset_from_sprout_data.pl  1.2  13 years  olson  Add license words.
load_literature.pl  1.3  13 years  olson  Add license words.
init_maps.pl  1.3  13 years  olson  Add license words.
add_assignments.pl  1.3  13 years  olson  Add license words.
generate_sprout_links.pl  1.2  13 years  olson  Add license words.
gi2fig.pl  1.3  13 years  olson  Add license words.
make_spreadsheet_and_notes.pl  1.3  13 years  olson  Add license words.
assign_synonym_ids_to_sims.pl  1.2  13 years  olson  Add license words.
make_sim_sets.pl  1.3  13 years  olson  Add license words.
get_best_set_of_genes_for_column.pl  1.3  13 years  olson  Add license words.
assign.pl  1.2  13 years  olson  Add license words.
p2p_daemon.pl  1.2  13 years  olson  Add license words.
generate_intergenic_blocks.pl  1.3  13 years  olson  Add license words.
package_raw_data_for_transplant.pl  1.2  13 years  olson  Add license words.
embl2gff.pl  1.20  13 years  olson  Add license words.
clustal_to_fasta.pl  1.2  13 years  olson  Add license words.
index_fasta.pl  1.2  13 years  olson  Add license words.
assign_to_sets.pl  1.5  13 years  olson  Add license words.
package_assignments.pl  1.8  13 years  olson  Add license words.
index_neighborhoods.pl  1.3  13 years  olson  Add license words.
filter_new_overlaps.pl  1.2  13 years  olson  Add license words.
bring_system_up_to_date.pl  1.2  13 years  olson  Add license words.
merge_annotations.pl  1.3  13 years  olson  Add license words.
genomes_of.pl  1.2  13 years  olson  Add license words.
build_access_sets.pl  1.2  13 years  olson  Add license words.
expand_blast_table.pl  1.2  13 years  olson  Add license words.
check_starts_for_peg_sets.pl  1.5  13 years  olson  Add license words.
is_bacterial.pl  1.2  13 years  olson  Add license words.
make_protein_sets.pl  1.4  13 years  olson  Add license words.
generate_input_for_auto_assignments.pl  1.2  13 years  olson  Add license words.
check_tbl.pl  1.2  13 years  olson  Add license words.
make_annotations_for_sprout.pl  1.12  13 years  olson  Add license words.
make_transferable_chunks.pl  1.4  13 years  olson  Add license words.
package_code.pl  1.2  13 years  olson  Add license words.
dump_attributes.pl  1.2  13 years  olson  Add license words.
make_jpg.pl  1.2  13 years  olson  Add license words.
make_phob_from_seqs.pl  1.7  13 years  olson  Add license words.
make_sprout_bbhs.pl  1.2  13 years  olson  Add license words.
check_changes_in_organisms.pl  1.2  13 years  olson  Add license words.
pegs.pl  1.3  13 years  olson  Add license words.
check_sims_syntax.pl  1.3  13 years  olson  Add license words.
extract_data_to_keep.pl  1.5  13 years  olson  Add license words.
mark_nr.pl  1.2  13 years  olson  Add license words.
insert.pl  1.2  13 years  olson  Add license words.
make_rates.pl  1.2  13 years  olson  Add license words.
import_external_sequences_step1.pl  1.8  13 years  olson  Add license words.
fasta_for_hypo.pl  1.2  13 years  olson  Add license words.
generate_max_clusters.pl  1.2  13 years  olson  Add license words.
make_binary.pl  1.2  13 years  olson  Add license words.
build_excel_gene_table.pl  1.3  13 years  olson  Add license words.
generate_kernel_css.pl  1.5  13 years  olson  Add license words.
expand_transferred_chunks.pl  1.4  13 years  olson  Add license words.
p2p_sync_from_remote.pl  1.4  13 years  olson  Add license words.
make_calls.pl  1.4  13 years  olson  Add license words.
assign_synonym_ids_to_nr.pl  1.2  13 years  olson  Add license words.
generate_subsys_tables_for_sprout.pl  1.8  13 years  olson  Add license words.
build_exemplar_fasta.pl  1.3  13 years  olson  Add license words.
make_occ_counts.pl  1.2  13 years  olson  Add license words.
align_with_clustal.pl  1.8  13 years  olson  Add license words.
fix_ext_funcs.pl  1.2  13 years  olson  Add license words.
import_subsystems.pl  1.22  13 years  olson  Add license words.
fig_xmlrpc_server.pl  1.5  13 years  olson  Add license words.
install_code.pl  1.2  13 years  olson  Add license words.
load_local_maps.pl  1.3  13 years  olson  Add license words.
build_protein_families.pl  1.5  13 years  olson  Add license words.
generate_pin_caches.pl  1.5  13 years  olson  Add license words.
list_genomes.pl  1.2  13 years  olson  Add license words.
peg_to_name.pl  1.4  13 years  olson  Add license words.
distribute_attributes.pl  1.11  13 years  olson  Add license words.
load_chromosomal_clusters.pl  1.2  13 years  olson  Add license words.
test_cv.expected  1.1  14 years  efrank   Basic regression test on CV stuff at FIG API level (which underlies CGI).
README  1.1.1.1  15 years  efrank   import

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