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File Rev. Age Author Last log entry
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sequence_dereplication.pl  1.1  11 years  arodri7  first version of sequence_dereplication. Script takes sequences which are subset...
connect_PDB_to_FIGfams_worker.pl  1.1  12 years  arodri7  update changes
make_md5_figfams_file.pl  1.1  11 years  arodri7  script makes the md5 to figfams file
get_NCBI_genome_attributes.pl  1.1  12 years  arodri7  get_NCBI_genome_attributes searches the NCBI internet sites for genome attribute...
get_FIGfams_SS_NMPDR_stats.pl  1.1  11 years  arodri7  *** empty log message ***
install_partition_reps.pl  1.2  10 years  arodri7  commit change
make_partition_reps_worker.pl  1.3  10 years  arodri7  commit change
make_subsys_based_families2.pl  1.1  10 years  arodri7  commit changes
create_ff_covering_skeleton.pl  1.2  11 years  arodri7  fixed script that creates a directory structure for a FIGfam for its sequence co...
propagate_subsys_changes_to_figfams.pl  1.12  10 years  arodri7  commit changes
assign_using_ff_original.pl  1.1  11 years  arodri7  original format of assign_using_ff
figfam_quality_control.pl  1.8  10 years  arodri7  commit changes
connect_PDB_to_FIGfams.pl  1.1  12 years  arodri7  update changes
assign_figfam.pl  1.1  11 years  arodri7  add original assign_using_ff
compare_figfam_release_results.pl  1.5  10 years  arodri7  commit changes
test_figfam_peg.pl  1.6  12 years  arodri7  update changes
make_partition_repsP.pl  1.4  10 years  arodri7  commit change
figfam_subsystems.pl  1.2  10 years  arodri7  commit changes
figfam_size_distribution.pl  1.1  12 years  arodri7  update changes
assign_using_ff.pl  1.9  10 years  arodri7  commit changes
reformat_circular_contigs.pl  1.1  11 years  arodri7  added reformat_circular_contigs for rapid_propagation_plasmids
assign_using_ff_parallel.pl  1.2  11 years  arodri7  made updates to functions used for updating FIGfams
cleanup_figfams_updates.pl  1.1  10 years  arodri7  commit changes
submit_ff_test.pl  1.6  10 years  arodri7  commit changes
update_FIGfams.pl  1.12  10 years  arodri7  commit changes
get_evaluation_check.pl  1.3  12 years  bartels  added option -a for showing pegs that do not match via blast
get_evaluation_check_rast_new_vs_old.pl  1.1  12 years  bartels   compare old rast with development version
Consistency_Families.pm  1.1  12 years  bartels  *** empty log message ***
recompute_comparison.pl  1.1  12 years  bartels  *** empty log message ***
make_tf_equivalog_file.pl  1.1  12 years  bartels  *** empty log message ***
merge_assignments.pl  1.1  11 years  bartels  *** empty log message ***
createTIGRfamSrc.pl  1.1  12 years  bartels  *** empty log message ***
set_not_private.pl  1.1  11 years  bartels  *** empty log message ***
server_paper_example7.pl  1.4  10 years  chenry  Corrected a few bugs in the example script.
FIGMODELscheduler.pl  1.3  10 years  chenry  Switched over the PPO as the system for holding the job queue tables.
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
compare_scenarios.pl  1.5  11 years  dejongh  Changes to move the 'All' scenarios directory to FIG_Config::global/Models/All
GeneSet_P_Values.R  1.3  9 years  dejongh  fixes
make_SBML_model.pl  1.6  11 years  dejongh  switch to scenario_directory
make_indexes.pl  1.17  10 years  dejongh  Fix KEGG location
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
accumulate_pegs_to_scenario_paths.pl  1.1  9 years  dejongh  determine which pegs in an organism are involved in which scenario paths
make_MPS_model.pl  1.7  11 years  dejongh  switch to scenario_directory
RunRMA.R  1.5  9 years  dejongh  preallocate no_match_pm_mm; delete no_match row at end
update_hope_info.pl  1.4  10 years  dejongh  added comments
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
load_kegg.pl  1.15  10 years  dejongh  Fix KEGG location
check_hope_info.pl  1.8  10 years  dejongh  updates to check for invalid maps and reaction/ec mismatches
check_model.pl  1.7  11 years  dejongh  switch to scenario_directory
make_probes_to_genes.pl  1.8  9 years  dejongh  check for same contig when matching probe to peg
analyze_scenario_connections.pl  1.4  11 years  dejongh  Changes to move the 'All' scenarios directory to FIG_Config::global/Models/All
update_kegg_data.pl  1.6  10 years  dejongh  removed comment
svr_gap_filled_reactions_and_roles.pl  1.5  9 years  devoid  fixing some problems with authentication, error reporting
svr_ids_to_subsystems.pl  1.6  9 years  disz  Added stderr output for non-matches
annotation_counts.pl  1.2  9 years  disz  Check in coming dates
svr_taxonomy.pl  1.2  9 years  disz  FIxed POD
svr_co_occurrence_evidence.pl  1.4  9 years  disz  FigFam 6 digit problem
add_structured_english.pl  1.4  12 years  disz  Added escape arg to structured engkish
find_poss_errs.pl  1.3  9 years  disz  FigFam 6 digit problem
build_new_figfam_release.pl  1.5  9 years  disz  FigFam 6 digit problem
svr_aliases_of.pl  1.6  9 years  disz  Added precise option
make_figfam_tree.pl  1.2  9 years  disz  FigFam 6 digit problem
server_paper_example2.pl  1.7  10 years  disz  Changed to use ANNO server
server_paper_example5.pl  1.3  10 years  disz  Switched to ANNO server
server_paper_example3.pl  1.5  10 years  disz  converted to new SAP server
seed2tbl.pl  1.3  9 years  disz  FigFam 6 digit problem
generate_partitions_worker.pl  1.4  9 years  disz  FigFam 6 digit problem
figfam.pl  1.23  9 years  disz  FigFam 6 digit problem
svr_file_to_spreadsheet.pl  1.2  9 years  disz  Fixed error message
build_prok_nonff_fasta.pl  1.4  9 years  disz  FigFam 6 digit problem
rapid_propagation_plasmid.pl  1.22  9 years  disz  FigFam 6 digit problem
install_partitions.pl  1.5  9 years  disz  FigFam 6 digit problem
generate_partitionsP.pl  1.6  9 years  disz  FigFam 6 digit problem
show_structured_english.pl  1.1  12 years  disz  Ross's code to generate annotations for NCBI
FFB2_get_oligos.pl  1.10  9 years  disz  FigFam 6 digit problem
initialize_figfams.pl  1.12  9 years  disz  FigFam 6 digit problem
rep_sets.pl  1.1  10 years  disz  Old code finally checked in to create representative sets
svr_spreadsheet_to_file.pl  1.2  9 years  disz  Fixed missing file error message
svr_evidence.pl  1.1  9 years  disz  New svr script to get evidence code
make_figfam_tree_worker.pl  1.2  9 years  disz  FigFam 6 digit problem
fc_figfams.pl  1.3  9 years  disz  FigFam 6 digit problem
test_figfam_placement_into_families.pl  1.10  9 years  disz  FigFam 6 digit problem
find_neighbors.pl  1.39  9 years  disz  FigFam 6 digit problem
ff.pl  1.7  9 years  disz  FigFam 6 digit problem
svr_protein_assertions.pl  1.6  10 years  disz  CHanged ACHserver to SAPserver and fixed processing of return values
README  1.1.1.1  16 years  efrank   import
test_cv.expected  1.1  14 years  efrank   Basic regression test on CV stuff at FIG API level (which underlies CGI).
svr_psiblast_search.pl  1.26  9 years  fangfang  remove debug lines
svr_align_seqs.pl  1.14  9 years  fangfang  add option --anysymbol
svr_cdd_scan.pl  1.2  9 years  fangfang  add more options
svr_motif.pl  1.4  9 years  fangfang  simplify code
svr_rRNA.pl  1.2  9 years  fangfang  update pod
svr_taxonomically_related_genomes.pl  1.10  9 years  fangfang  update POD
svr_trim_ali.pl  1.10  9 years  fangfang  fix description field in trim html
fetch_models_for_genomes.pl  1.1  9 years  fangfang  initial import
svr_tree_to_html.pl  1.12  9 years  fangfang  modify option gray
svr_insert_seqs_into_alignment.pl  1.2  9 years  fangfang  take advantage of gjoseqlib's flexible API to implicitly interact with STDIN/STD...
at.pl  1.3  9 years  fangfang  update
svr_ali_to_html.pl  1.2  9 years  fangfang  added SAS header
svr_link_to_compare_regions.pl  1.4  9 years  fangfang  fixed typo in $genomeH
svr_cohesion_groups.pl  1.4  9 years  fangfang  update
svr_tree.pl  1.10  9 years  fangfang  add parallel support for bootstrap
svr_find_fused_genes.pl  1.3  9 years  fangfang  updated POD
run_model_generation_all.pl  1.1  12 years  formsma  This script will generate models for all complete genomes in the seed. - Kevin
predict_scenarios.pl  1.2  12 years  formsma  Added code to automatically run 'run_scenarios All' if it hasn't been run. These...
call_genome_using_glimmer.pl  1.3  11 years  gdpusch  Rewrite to remove overlap removal.
svr_seed_to_genbank.pl  1.2  9 years  gdpusch  Fixed use of "package" when I meant "use." :(
remove_embedded_pegs.pl  1.19  9 years  gdpusch  Modified to use Kmers.
svr_genbank_to_seed.pl  1.1  9 years  gdpusch  SVR GenBank parser using Gary\'s code
reformat_contigs.pl  1.24  9 years  gdpusch  Fixed contig-ID "0" bug
build_figfam_pssm_db.pl  1.2  13 years  gdpusch  Major modifications to &load_family_ids()
svr_update_assignments.pl  1.3  10 years  gdpusch  Fixed typo.
backfill_gaps.pl  1.20  10 years  gdpusch  Added check to make sure comparison genome exists, in case RAST and OTU servers ...
add_rbs_data_for_start_predictions.pl  1.3  12 years  gdpusch  Added FIGV support. -- /gdp
order_corrections_for_start_predictions.pl  1.5  12 years  gdpusch  Added FIGV support. -- /gdp
feature_length_histogram.pl  1.3  12 years  gdpusch  Fixed duplicated ID bug, plus minor cosmetic changes. -- /gdp
get_fasta_for_tbl_entries.pl  1.11  10 years  gdpusch  Modified to remove complaints about uninitialed values when TBL entry does not c...
add_sim_data_for_start_predictions.pl  1.8  12 years  gdpusch  Added FIGV support. -- /gdp
svr_submit_RAST_job.pl  1.13  9 years  gdpusch  Added default value for bioname.
svr_seed_to_table.pl  1.3  9 years  gdpusch  Fixed typo in POD section.
get_dna.pl  1.6  12 years  gdpusch  Minor cosmetic change. -- /gdp
get_sims_for_start_predictions.pl  1.5  12 years  gdpusch  Added FIGV support. -- /gdp
rapid_propagation4.pl  1.7  9 years  gdpusch  Fixed problem with virus/plasmid branch in "keep_genecalls" mode.
assess_completeness.pl  1.9  11 years  gdpusch  Fixed leading-whitspace bug.
find_approx_neigh.pl  1.6  9 years  gdpusch  Modified to look for "proposed_functions" and "proposed_non_ff_functions" as wel...
verify_genome_directory.pl  1.42  9 years  gdpusch  Added recognition of "contig.properties" file.
svr_tab2html.pl  1.5  9 years  gdpusch  Fixed a bug I introduced, and added a "--border" option to the table.
svr_assign_using_figfams.pl  1.11  9 years  gdpusch  Fixed "die" statement that lacks any conditional.
predict_starts.pl  1.8  12 years  gdpusch  Added FIGV support. -- /gdp
start_data_for_set_of_pegs.pl  1.6  12 years  gdpusch  Added FIGV support. -- /gdp
correct_frameshifts.pl  1.25  9 years  gdpusch  Replaced dies with warn and exit if '-nofatal', so that script fails gracefully ...
svr_genbank_to_table.pl  1.2  9 years  gdpusch  Added various alias IDs to output.
to_genbank.pl  1.7  9 years  gdpusch  Fixed bug handling 5S.
run_glimmer2.pl  1.7  13 years  gdpusch  Added support for multiple genetic codes. -- /gdp
build_initial_objects_for_start_predictions.pl  1.12  12 years  gdpusch  Modified to also work on new genomes using "FIGV.". -- /gdp
remove_rna_overlaps.pl  1.10  12 years  gdpusch  Added setting of VERBOSE from metafile. -- /gdp
make_overlap_report.pl  1.21  9 years  gdpusch  Fixed major bug handling negative strand; also minor cosmetic changes for readab...
add_start_data_for_start_predictions.pl  1.4  12 years  gdpusch  Added FIGV support. -- /gdp
rapid_propagation2.pl  1.5  9 years  gdpusch  Minor cosmetic changes.
extract_metagene_contigs.pl  1.12  9 years  gdpusch  Updated search for executables to revised software environment.
find_gaps.pl  1.9  11 years  gdpusch  Fixed (hopefully) incorrectly handled out-of-bounds cases.
get_potential_starts_for_start_predictions.pl  1.3  12 years  gdpusch  Added FIGV support. -- /gdp
extract_DNA_for_whole_ORFs.pl  1.4  11 years  gdpusch  Fixed possible DNA case sensitivity.
pull_orfs.pl  1.7  9 years  gdpusch  Corrected regexp error.
make_genome_dir_for_close.pl  1.9  12 years  gdpusch  Fixed handling of spliced loci. -- /gdp
promote_orfs_to_pegs.pl  1.15  9 years  gdpusch  Code restructured, and modified to fail gracefully if there are no closest genom...
find_special_proteins.pl  1.4  11 years  gdpusch  Suppress writing "called_by" and "special_pegs" when "-keep" is selected. -- /gd...
renumber_features.pl  1.13  9 years  gdpusch  Modified a debugging statement.
parse_genbank.pl  1.33  9 years  gdpusch  Added "-user_trans_only" flag.
find_miscalled_genes.pl  1.4  9 years  gdpusch  Added check to make sure nonref gene is not already in a subsystem.
svr_compare_feature_tables.pl  1.7  9 years  gdpusch  Fixed typo in variable-name
make_calls_for_start_predictions.pl  1.4  12 years  gdpusch  Added FIGV support. -- /gdp
svr_inherit_annotations.pl  1.2  9 years  gdpusch  Checkin of (hopefully) production version
svr_align_using_muscle.pl  1.2  9 years  gdpusch  Fixed incorrect function names.
genome_peg_dna.pl  1.3  12 years  golsen  Extensive modifications to allow more options, and handle large genomes by not r...
modify_tree.pl  1.1  9 years  golsen  A general purpose tree modification utility.
align_fasta.pl  1.3  10 years  golsen  Add support for alignment with muscle.
find_SEED_SSU_rRNA_genes.pl  1.4  11 years  golsen  Add type field to output report (always rna).
assign_to_unchanged.pl  1.3  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
insert_prot_into_tree.pl  1.14  13 years  golsen  Continuing the update of tree packages and programs
add_to_alignment.pl  1.8  9 years  golsen  Fix the libraries used for I/O.
collect_related_sequences.pl  1.3  13 years  golsen  Encapsulate all of the SEED-dependent functions in the perl module. It should st...
add_prots_to_tree.pl  1.1  13 years  golsen  New script for adding proteins to an existing tree.
align_with_clustal_2.pl  1.4  13 years  golsen  Trivial format change.
sketch_tree.pl  1.3  9 years  golsen  Many changes and updates.
load_dlits.pl  1.5  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
jgi_data_merge.pl  1.2  9 years  golsen  Fix the taxonomy to use NCBI full taxonomy if TAXONOMY does not exist.
sync_new_system.pl  1.6  14 years  golsen  Just adding a newline at end of file to make repository match my working copy. ...
export_dlits.pl  1.2  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
run_muscle.pl  1.3  9 years  golsen  Update libraries used.
fig_net.pl  1.4  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
svr_translations_of.pl  1.6  9 years  golsen  Add an option of genome names in the output. Clean up the way functions are adde...
make_proml_tree.pl  1.6  13 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
gd_tree.pl  1.1  11 years  golsen  Add a command line program to make a png graphic from a newick tree file.
generate_similarities.pl  1.3  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
Simple.pl  1.4  14 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
find_selenoproteins.pl  1.4  12 years  golsen  Add functions to reference selenoproteins, and add change the set slightly. Rep...
make_protein_weights_and_rates.pl  1.2  13 years  golsen  Moving some tree building tools into packages.
svr_sims2html.pl  1.6  9 years  golsen  Add pod documentation.
make_proml_tree_0.pl  1.1  13 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
svr_NCBI_taxonomy.pl  1.2  9 years  golsen  Add more formats in which abbreviated lineages can be returned. Add long form of...
test_parse_gff.pl  1.3  14 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
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...
index_sims_file.c  1.7  11 years  golsen  Bob added an #include <sys/types.h>. This is committing that code change.
alignment_to_html.pl  1.2  10 years  golsen  Minor updates.
find_protein_homologs.pl  1.1  12 years  golsen  Debugging and adding support of all the NCBI genetic codes.
fig_rpc.pl  1.4  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
compute_extra_dlit_data.pl  1.4  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
get_taxid_journals.pl  1.1  13 years  hwang  get journals from PMC using taxide
explore_subsys_pmid.pl  1.5  13 years  hwang  PEG information is no longer stored in the file. Parsing of the file in this scr...
to_arabidopsis.pl  1.1  13 years  hwang  This script parses arabidopsis.org to get the AT aliases output
get_pubmed_journals.pl  1.5  13 years  hwang  update comment that this is for peg curation
subsys2pubmed.pl  1.4  13 years  hwang  change script to add new attribute after each subsystem versus after all subsyst...
get_journals_for_frole.pl  1.1  13 years  hwang  Files to get journal information from PubMed
to_org_specific.pl  1.4  13 years  hwang  fix syntax error
get_journals_for_org.pl  1.1  13 years  hwang  this script is the backend to get journals using taxonomy id or name. This calls...
peg2pubmed.pl  1.1  13 years  hwang  Added two scripts that will generate pubmed files
meta.pl  1.12  10 years  jared  added update_path
WebAppBackend.pl  1.2  11 years  jared  make user and org commands case insensitive
make_interpro_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
make_PDB_attributes.pl  1.2  13 years  mkubal  fix to score format
make_Ontology_database.pl  1.3  12 years  mkubal  provides usage when no argument given
make_go_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
compute_PCA_with_metagenomes_as_variables.pl  1.1  11 years  mkubal  called by PCA_mgav
prepare_metagenome_files_for_download.pl  1.4  12 years  mkubal  full loop
prepare_metagenome_files_for_ftp.pl  1.3  12 years  mkubal  checks for PUBLIC file
make_prosite_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
make_Phobius_attributes.pl  1.2  12 years  mkubal  added date as 2nd argument
parse_uniparc.pl  1.1  12 years  mkubal  v1
compute_mw_and_pi_with_BioPerl.pl  1.1  12 years  mkubal  computes mw and pi for all pegs in complete genomes
compute_crc64_for_all_pegs.pl  1.1  12 years  mkubal  v1
run_remote_Phobius_for_fasta.pl  1.1  12 years  mkubal  fasta file as input
make_SignalP_attributes.pl  1.2  13 years  mkubal  changed ; to :: for key separator
compute_CELLO_and_TMPRED.pl  1.2  13 years  mkubal  test for dir exist
make_CDD_attributes.pl  1.2  13 years  mkubal  fix to score format
mg_user_id_to_unique.pl  1.2  12 years  mkubal  full loop
make_cdd_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
make_pir_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
blast_pdb_against_nr_on_tla.pl  1.1  13 years  mkubal  blast pdb against nr
compute_PCA_for_metagenomes.pl  1.1  11 years  mkubal  called by PCA_ssav
make_PFAM_HMM_derived_attributes.pl  1.2  12 years  mkubal  added date as 2nd argument
make_IPR_PFAM_GO_attributes.pl  1.3  13 years  mkubal  fix to score format
submit_genome_to_signalP.pl  1.2  13 years  mkubal  test for dir exist
crc64.py  1.1  12 years  mkubal  uses for mapping of interpro downlaod to pegs
run_HMM_search_on_timelogic.pl  1.1  12 years  mkubal  version 1.0
submit_to_iprscan_on_biocluster.pl  1.1  13 years  mkubal  run iprscan on cluster
compute_mw_and_pi.pl  1.2  13 years  mkubal  one genome at a time
run_remote_Phobius_for_genome.pl  1.1  12 years  mkubal  for single genome
make_CELLO_and_TMPRED_attributes.pl  1.2  13 years  mkubal  changed ; to :: for key separator
submit_genome_to_rpsblast_against_CDD_on_biocluster.pl  1.2  13 years  mkubal  test for dir exist
metagenome2genbank.pl  1.4  12 years  mkubal  includes data from meta.xml
run_remote_PHOBIOUS.pl  1.1  12 years  mkubal  runs Phobius computation for given geneome
make_pdb_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
test_Observation.pl  1.1  13 years  mkubal  for testing
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
add_figbar_and_genome_attributes.pl  1.1  12 years  mkubal  v1
make_pfam_ontology.pl  1.4  12 years  mkubal  provides usage when no argument given
make_PROSITE_PIR_PRODOM_attributes.pl  1.3  13 years  mkubal  fix to score format
format_peg_dbs.pl  1.3  14 years  olson  Add license words.
index_sprout.pl  1.12  14 years  olson  Add license words.
export_subsystem_as_gff.pl  1.2  14 years  olson  Add license words.
update_PSEED_subsystems.pl  1.3  9 years  olson  add doc
run_start_predictions_for_all_subsystems.pl  1.4  14 years  olson  Add license words.
relevant_pchsG.pl  1.4  14 years  olson  Add license words.
compute_new_ids.pl  1.2  14 years  olson  Add license words.
build_nohit_fasta.pl  1.2  14 years  olson  Add license words.
SplitGeneSets.R  1.2  9 years  olson  Update to expression pipeline code
FFB2_usable_motifs.pl  1.4  9 years  olson  Update to FF processing
count_bases.pl  1.2  14 years  olson  Add license words.
generate_Property_for_sprout.pl  1.6  14 years  olson  Add license words.
package_annotations.pl  1.9  14 years  olson  Add license words.
call_coregulated_clusters_on_chromosome.pl  1.7  9 years  olson  Update to expression pipeline code
check_starts_for_pegs.pl  1.5  14 years  olson  Add license words.
fill_in_roles.pl  1.4  14 years  olson  Add license words.
index_annotations.pl  1.11  12 years  olson  bugfix
update_sims.pl  1.13  14 years  olson  Add license words.
is_prokaryotic.pl  1.2  14 years  olson  Add license words.
get_class_examples.pl  1.2  14 years  olson  Add license words.
boot_cluster_seed.pl  1.5  14 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
show_reconfig_cmd.pl  1.3  14 years  olson  Add license words.
split_sims.pl  1.3  14 years  olson  Add license words.
install_assignments.pl  1.7  14 years  olson  Add license words.
merge_missing_gene_output.pl  1.3  9 years  olson  bugfix
make_subsystems_from_clusters.pl  1.5  14 years  olson  Add license words.
sp2fasta.pl  1.2  14 years  olson  Add license words.
make_reduce_sims_index.pl  1.1  12 years  olson  new script
register_features_with_clearinghouse.pl  1.2  14 years  olson  Add license words.
changed_starts.pl  1.7  14 years  olson  Add license words.
order_sets.pl  1.3  14 years  olson  Add license words.
assign_towards_subsystems.pl  1.2  14 years  olson  Add license words.
FFB2_create_binary_relationships.pl  1.1  9 years  olson  New FIGfam merge code.
load_bbhs.pl  1.15  12 years  olson  *** empty log message ***
filter_pegs_in_subsystems.pl  1.4  14 years  olson  Add license words.
FFB2_make_family_vector.pl  1.1  9 years  olson  compute family.vector.def for a figfam direcotry.
extract_data_for_syncing_after_update.pl  1.6  14 years  olson  Add license words.
clean_subsystems.pl  1.2  14 years  olson  Add license words.
find_rnas.pl  1.2  10 years  olson  fix ANNOserver args
dna_seq.pl  1.2  14 years  olson  Add license words.
complete_genomes.pl  1.7  14 years  olson  Add license words.
index-pegsyn2.pl  1.1  12 years  olson  new version of pegsyn indexer that presorts data before inserting into the btree...
load_links.pl  1.7  11 years  olson  Only load links from files ending in "links" (rather than files with it anywhere...
build_alignments_for_subsystems.pl  1.4  14 years  olson  Add license words.
load_external_orgs.pl  1.3  14 years  olson  Add license words.
run_start_predictions_for_spreadsheet.pl  1.6  14 years  olson  Add license words.
svr_column_of_subsystem.pl  1.1  10 years  olson  server script to pull a subsystem colum
index_contig_files.c  1.5  14 years  olson  fix to work on 64-bit linux
md5.c  1.3  14 years  olson  Doh, put proper comments in for C code.
svr_run_RAST_jobs.pl  1.6  9 years  olson  Add --determineFamily
compute_PSEED_reconstructions.pl  1.2  9 years  olson  More fixups.
check_lost_sims.pl  1.2  14 years  olson  Add license words.
flip_sims.pl  1.7  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
compute_dbdir_checksum.pl  1.3  14 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
build_sas_distro.pl  1.7  9 years  olson  mods for building myRAST
find_genes_based_on_neighbors_par.pl  1.1  10 years  olson  parallel version of find_genes_based_on_neighbors
sprout_search.pl  1.2  14 years  olson  Add license words.
init_peg_job_scheduler.pl  1.4  14 years  olson  Add license words.
gff2ncbitab.pl  1.3  12 years  olson  add swissprot
make_attribute_index.pl  1.6  14 years  olson  Add license words.
get_nr_entries_without_sims.pl  1.4  14 years  olson  Add license words.
split_and_install_pchs.pl  1.2  14 years  olson  Add license words.
postprocess_computed_sims.pl  1.2  14 years  olson  Add license words.
generate_GenomeGroups_for_sprout.pl  1.3  14 years  olson  Add license words.
build_nr_sources.pl  1.14  13 years  olson  Rollup of various rast-related changes.
clustal2fasta.pl  1.2  14 years  olson  Add license words.
FFB2_xx.pl  1.1  10 years  olson  Bunch of figfam generation optimizations.
questionable_calls.pl  1.2  14 years  olson  Add license words.
select_genomes_for_sprout.pl  1.2  14 years  olson  Add license words.
synchronize_annotations_and_assignments.pl  1.2  14 years  olson  Add license words.
verify_pegs_in_tbl.pl  1.2  14 years  olson  Add license words.
remove_clustered_pchs2.pl  1.1  13 years  olson  Missing scripts.
blastn_seqs.pl  1.2  14 years  olson  Add license words.
cluster_by_sim.pl  1.2  14 years  olson  Add license words.
test_cv.pl  1.2  14 years  olson  Add license words.
bbhs.pl  1.7  14 years  olson  Add license words.
load_sets.pl  1.5  14 years  olson  Add license words.
compute_pins_and_clusters.pl  1.2  14 years  olson  Add license words.
db_xrefs_of.pl  1.4  14 years  olson  Add license words.
validate_subsystem.pl  1.2  14 years  olson  Add license words.
validate_genome_gff.pl  1.6  14 years  olson  Add license words.
external_calls.pl  1.2  14 years  olson  Add license words.
assign_using_kmers.pl  1.8  10 years  olson  Add support for explicitly specifying FRI.db, setI.db, table.binary
gff2Ontology.pl  1.4  14 years  olson  Add license words.
remove_sims_not_in_nr.pl  1.1  13 years  olson  Missing scripts.
update_uniq_id_data.pl  1.7  13 years  olson  use function_of_quick
compute_simple_scores.pl  1.4  14 years  olson  Add license words.
make_sp_func_syn_dicts.pl  1.2  14 years  olson  Add license words.
pegs_in_conflict.pl  1.3  14 years  olson  Add license words.
break_scaffolds.pl  1.2  14 years  olson  Add license words.
insert_all.pl  1.2  14 years  olson  Add license words.
run_fc.pl  1.2  14 years  olson  Add license words.
check_alignment.pl  1.2  14 years  olson  Add license words.
apply_peg_changes_to_subsystem.pl  1.3  14 years  olson  Add license words.
load_pch_pins.pl  1.2  14 years  olson  Add license words.
test_generate_anno_gff.pl  1.3  14 years  olson  Add license words.
gather_attributes.pl  1.8  14 years  olson  Add license words.
maint-remove-obsolete-aliases.pl  1.1  13 years  olson  Missing scripts.
get_pathways_for_EC.pl  1.2  14 years  olson  Add license words.
fix_annotations.pl  1.2  14 years  olson  Add license words.
ali_to_seq.pl  1.2  14 years  olson  Add license words.
FFB2_merge_oligos.pl  1.4  9 years  olson  Update to FF processing
compute_fasta_lengths.pl  1.1  9 years  olson  Precompute fasta lengths for the non-FF nr.
exec-cgi.pl  1.1  10 years  olson  cgi executor for mac rast
display_tree.pl  1.4  14 years  olson  Add license words.
relabel_nodes.pl  1.2  14 years  olson  Add license words.
make_transferable_tarfiles.pl  1.3  14 years  olson  Add license words.
build_anno_clearinghouse.pl  1.6  12 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
all_subsystems.pl  1.2  14 years  olson  Add license words.
check_for_unique_sims.pl  1.2  14 years  olson  Add license words.
assess_gene_call_quality.pl  1.14  9 years  olson  don't write the overlap report to metadata log; it is very large.
blast_request.pl  1.2  14 years  olson  Add license words.
location_of.pl  1.2  14 years  olson  Add license words.
stop_services.pl  1.5  14 years  olson  Add license words.
process_sim_deletions_and_replacements.pl  1.3  14 years  olson  Add license words.
cat_spreadsheet.pl  1.2  14 years  olson  Add license words.
make_match_table.pl  1.2  14 years  olson  Add license words.
restrict_by_similarity.pl  1.4  14 years  olson  Add license words.
aliases_of.pl  1.6  14 years  olson  Add license words.
make_peg_maps_from_fasta.pl  1.2  11 years  olson  need to compute sims both directions because connections_between now uses bbhs.
make_PHOBs_for_subsystems.pl  1.5  14 years  olson  Add license words.
lengths_of_contigs.pl  1.2  14 years  olson  Add license words.
check_peg_assignments.pl  1.3  14 years  olson  Add license words.
Pipeline.R  1.4  9 years  olson  Update to expression pipeline code
find_genes_based_on_neighbors.pl  1.24  10 years  olson  Switch to FFs and FF instead of FigFams and FigFam
sequence_length_histogram.pl  1.6  9 years  olson  Include in SAS
remove_clustered_pchs3.pl  1.1  13 years  olson  Missing scripts.
install_features_batch.pl  1.1  12 years  olson  Add new script to install a batch of genomid.tbl / genomeid.fasta files. Initial...
analyze_kmer_assignments.pl  1.1  10 years  olson  new script to compare output of assign_using_kmers to current SEED assignments
embl2gff_addmd5.py  1.2  14 years  olson  Add license words.
make_assignments_set.pl  1.3  14 years  olson  Add license words.
seed_run_job.pl  1.4  13 years  olson  readonly fixes; seed-run-job update to run from input file
similar_to.pl  1.4  14 years  olson  Add license words.
initial_set.pl  1.2  14 years  olson  Add license words.
seed_job_scheduler.pl  1.3  14 years  olson  Add license words.
install_translation_rules.pl  1.3  14 years  olson  Add license words.
index_translations.pl  1.24  9 years  olson  Add index on fileno.
generate_pinned_homologs.pl  1.2  14 years  olson  Add license words.
apply_map.pl  1.2  14 years  olson  Add license words.
extract_DNA_sequence_from_object_for_start_predictions.pl  1.2  14 years  olson  Add license words.
build_nr.pl  1.22  12 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
alter_tbl.pl  1.4  14 years  olson  Add license words.
merge_translation_rules.pl  1.7  14 years  olson  Add license words.
extend_subsystem.pl  1.2  14 years  olson  Add license words.
reformat_sims.pl  1.8  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
map_sims.pl  1.5  14 years  olson  Add license words.
macapp_files_to_genome_dir.pl  1.2  9 years  olson  Banish cp.
write_go_mappings.pl  1.2  9 years  olson  More fixups.
package_sims.pl  1.2  14 years  olson  Add license words.
fasta_to_phylip.pl  1.2  14 years  olson  Add license words.
install_lightweight_code.pl  1.2  14 years  olson  Add license words.
upstream.pl  1.3  14 years  olson  Add license words.
start_dbserver.pl  1.2  14 years  olson  Add license words.
cluster_by_bbhs.pl  1.2  14 years  olson  Add license words.
renumber_seed_dir.pl  1.4  10 years  olson  Don't fail if Features dir does not exist.
root_at.pl  1.2  14 years  olson  Add license words.
assign_to_hypo.pl  1.3  14 years  olson  Add license words.
import_external_sequences_step3.pl  1.5  14 years  olson  Add license words.
load_sims.pl  1.10  14 years  olson  If we are loading unmapped files (as generated by make_close -no-map and make_s...
load_id_correspondence.pl  1.3  12 years  olson  updates to the load_id_correspondence loader and searching code.
project.pl  1.2  14 years  olson  Add license words.
alias2fig.pl  1.2  14 years  olson  Add license words.
valid_fasta_file.pl  1.1  10 years  olson  Check to ensure a fasta file is valid.
assign_with_no_sims.pl  1.2  14 years  olson  Add license words.
get_ON_probes.pl  1.4  9 years  olson  expression fixes
load_ec_names.pl  1.6  11 years  olson  support for change in format to the KEGG/ECtable.
tabs2rel.pl  1.2  14 years  olson  Add license words.
is_archaeal.pl  1.2  14 years  olson  Add license words.
generate_Source_for_sprout.pl  1.2  14 years  olson  Add license words.
fasta_cksum.c  1.4  14 years  olson  Doh, put proper comments in for C code.
salvage_annotations.pl  1.6  14 years  olson  bugfix.
roles_in_subsystem.pl  1.2  14 years  olson  Add license words.
to_map_coords.pl  1.3  14 years  olson  Add license words.
peg_to_pdb.py  1.2  14 years  olson  Add license words.
rapid_propagation3.pl  1.10  9 years  olson  Support family determiantion.
extract_genes.pl  1.5  14 years  olson  Add license words.
clean_sims.pl  1.2  14 years  olson  Add license words.
FFB2_compute_relationships_for_genera.pl  1.1  9 years  olson  New FIGfam merge code.
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 ...
compute_pchs_from_sims.pl  1.2  13 years  olson  Rollup of changes for the new RAST install.
dump_machine_state.pl  1.3  14 years  olson  Add license words.
extract_sp_links.pl  1.3  13 years  olson  fix -h error
svr_delete_RAST_job.pl  1.3  10 years  olson  Fix 666666 problem. Add support for using the test server.
condense_blast.pl  1.2  14 years  olson  Add license words.
make_fig_files.pl  1.3  14 years  olson  Add license words.
assign_synonym_ids.pl  1.2  14 years  olson  Add license words.
reformat_timelogic_sims.pl  1.2  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
generate_ilits.pl  1.3  9 years  olson  fix for FFs changes
generate_genome_feature_tables_for_sprout.pl  1.16  14 years  olson  Add license words.
get_empty_ecs.pl  1.4  14 years  olson  Add license words.
rapid_propagation.pl  1.75  11 years  olson  use $num_neighbors internally instead of hardwired constant
make_sprout_upstream.pl  1.2  14 years  olson  Add license words.
load_atomic_regulons.pl  1.1  9 years  olson  initial atomic regulon table loader
parse_mart.py  1.6  14 years  olson  Add license words.
FFB2_families_in_subsystems.pl  1.1  9 years  olson  Update to FF processing
load_distances.pl  1.5  14 years  olson  Add license words.
make_maps_from_sub.py  1.5  14 years  olson  Add license words.
run_peg_job_worker.pl  1.4  14 years  olson  Add license words.
index_feature_dir_fasta.pl  1.1  12 years  olson  Index scripts for FIGV accleration.
keep_only.pl  1.2  14 years  olson  Add license words.
add_close_genes.pl  1.2  14 years  olson  Add license words.
FFB2_usable_motifs2.pl  1.3  9 years  olson  Update to figfam build code
build_dtr_distro.pl  1.1  9 years  olson  new script
map_sims_for_bigfc.pl  1.2  14 years  olson  Add license words.
index_sims.pl  1.12  11 years  olson  Bump id size.
make_sp_org_domain_table.pl  1.2  14 years  olson  Add license words.
get_empty_ecs  1.3  14 years  olson  Add license words.
expand_multifunctional_roles.pl  1.3  14 years  olson  Add license words.
load_hugo.pl  1.6  14 years  olson  Add license words.
index_subsystems.pl  1.13  9 years  olson  fix ss indexing
fix_eol.pl  1.2  14 years  olson  Add license words.
peg_to_subsystems.pl  1.3  14 years  olson  Add license words.
package_translation_rules.pl  1.2  14 years  olson  Add license words.
generate_gene_blocks.pl  1.3  14 years  olson  Add license words.
to_prodom.pl  1.7  10 years  olson  fix updated URL
remove_multiple_occurring_probes.pl  1.2  9 years  olson  exp fixes
to_insert.pl  1.2  14 years  olson  Add license words.
FFB2_load_memcache.pl  1.7  9 years  olson  Update to figfam build code
where_does_seq_hit.pl  1.2  14 years  olson  Add license words.
FFB2_update_FIGfams.pl  1.16  9 years  olson  fix memcache stuff
install_new_coupling_data.pl  1.3  12 years  olson  add option to install from a jobdir
install_anticipated_functions.pl  1.3  12 years  olson  Introduct &FIG::get_figfams_data()
make_phob_from_ids.pl  1.3  14 years  olson  Add license words.
init_dbserver.pl  1.3  14 years  olson  Add license words.
fill_in_cell.pl  1.2  14 years  olson  Add license words.
FFB2_merge_families_based_on_genus_groups.pl  1.3  9 years  olson  Big round of figfam update changes
make_peg_map_from_tbl.pl  1.3  11 years  olson  fix bug that made empty output
FFB2_build_ff_indexes.pl  1.1  10 years  olson  Rollup of figfam update fixes
map-nr-ids-to-ncbi-std.pl  1.1  12 years  olson  Script to map IDs in a SEED NR into forms acceptable to the indexed NCBI fasta p...
process_one_exp_dir.pl  1.4  9 years  olson  fix typo
FFB2_run_tests.pl  1.3  9 years  olson  Update to figfam build code
package_lightweight_code.pl  1.2  14 years  olson  Add license words.
genbank2gff3.pl  1.5  14 years  olson  Add license words.
paint_tree.pl  1.3  14 years  olson  Add license words.
make_sp_org_table.pl  1.2  14 years  olson  Add license words.
find_neighbors_using_figfams.pl  1.11  10 years  olson  Switch to FFs and FF instead of FigFams and FigFam
potentially_cotranscribed.pl  1.2  14 years  olson  Add license words.
sphinx_index_genome.pl  1.9  9 years  olson  index contig ids with genomes
FFB2_make_subsys_based_families.pl  1.3  9 years  olson  Big round of figfam update changes
p2p_sync_cron.pl  1.3  14 years  olson  Add license words.
FFB2_xy.pl  1.1  9 years  olson  Update to FF processing
possibly_truncated.pl  1.2  14 years  olson  Add license words.
fill_subsys.pl  1.5  14 years  olson  Add license words.
install_subsystems.pl  1.2  14 years  olson  Add license words.
run_rabbit_daemon.pl  1.1  9 years  olson  Driver script for running one of the RabbitMQ broker-based daemons.
delete_genomes_from_sims.pl  1.2  14 years  olson  Add license words.
set_to_relation.pl  1.2  14 years  olson  Add license words.
match_dna_to_aligned_prots.pl  1.4  14 years  olson  Add license words.
export_genome_as_gff.pl  1.6  14 years  olson  Add license words.
compute_contig_md5.pl  1.4  13 years  olson  rollup of metagenome server changes
compare_tree_and_alignment.pl  1.2  14 years  olson  Add license words.
compute_genome_similarity.pl  1.1  13 years  olson  Missing scripts.
restore_annotations.pl  1.2  14 years  olson  Add license words.
svr_kill_RAST_job.pl  1.4  10 years  olson  fix usage message
check_nr_and_peg_synonyms.pl  1.2  14 years  olson  Add license words.
fid2dna.pl  1.2  14 years  olson  Add license words.
find_maximal_clusters.pl  1.2  14 years  olson  Add license words.
Makefile.cprogs  1.2  12 years  olson  Support compilation of nap.c
pull_sp_entries.pl  1.2  14 years  olson  Add license words.
get_neighbors_and_corr_to_ref.pl  1.7  9 years  olson  remove cat and shell usage.
svr_SAP.t  1.4  10 years  olson  update tests
best_hits.pl  1.2  14 years  olson  Add license words.
fusion_of.pl  1.2  14 years  olson  Add license words.
html_parser.py  1.2  14 years  olson  Add license words.
interval.pl  1.2  14 years  olson  Add license words.
update-caches.pl  1.1  13 years  olson  Update SEED caches.
load_features.pl  1.24  12 years  olson  fix tmp file name.
FFB2_compare_tests.pl  1.4  9 years  olson  Update to figfam build code
svr_copy_to_RAST_dir.pl  1.3  10 years  olson  fix
register_genome_with_clearinghouse.pl  1.1  13 years  olson  Missing scripts.
get_long_enough.pl  1.2  14 years  olson  Add license words.
make_sp_desc_with_org.pl  1.2  14 years  olson  Add license words.
check_fast_sims.pl  1.2  14 years  olson  Add license words.
index_nr.pl  1.2  13 years  olson  compute length btree also
start_services.pl  1.12  14 years  olson  Add license words.
compute_genome_counts.pl  1.25  11 years  olson  Fix bug where compute_genome_counts fails to run on a genome directory with mult...
install_annotations.pl  1.4  14 years  olson  Add license words.
sort_and_split_bbhs.pl  1.5  12 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
das_test.pl  1.2  14 years  olson  Add license words.
install_feature_updates.pl  1.2  14 years  olson  Add license words.
check_all_lost_sims.pl  1.2  14 years  olson  Add license words.
load_wikipedia.pl  1.1  10 years  olson  Wikipedia cache loader.
to_gg.pl  1.2  14 years  olson  Add license words.
create_sims_btree.pl  1.1  14 years  olson  BTREE-index versions of these. Experimental still.
is_eukaryotic.pl  1.2  14 years  olson  Add license words.
make_assignments_fit_initial_css.pl  1.4  14 years  olson  Add license words.
build_syn.pl  1.2  14 years  olson  Add license words.
extract_subset_from_sprout_data.pl  1.2  14 years  olson  Add license words.
index_pins.pl  1.3  14 years  olson  new pin indexer
load_literature.pl  1.3  14 years  olson  Add license words.
get_PSEED_assignment_updates.pl  1.5  9 years  olson  More fixups.
index_anno_clearinghouse.pl  1.3  12 years  olson  multiple id support, build fixes
init_maps.pl  1.3  14 years  olson  Add license words.
add_assignments.pl  1.3  14 years  olson  Add license words.
compute_figfam_assignments.pl  1.2  9 years  olson  Clean up debugging, write concatenated output file.
generate_sprout_links.pl  1.2  14 years  olson  Add license words.
init_FIG.pl  1.13  9 years  olson  fixes for when dbhost is set
gi2fig.pl  1.3  14 years  olson  Add license words.
load_peg_mapping.pl  1.12  9 years  olson  Caching / FCGI speedup modifications.
index_figv_annos.pl  1.1  12 years  olson  Index scripts for FIGV accleration.
check_figfams.pl  1.6  12 years  olson  Introduct &FIG::get_figfams_data()
restrict_to_genomes.pl  1.3  14 years  olson  Add license words.
translate.pl  1.2  14 years  olson  Add license words.
make_spreadsheet_and_notes.pl  1.3  14 years  olson  Add license words.
test_figfam_FF_peg.pl  1.3  12 years  olson  Missed one of the figfamdata fixes.
FFB2_create_binary_kmers.pl  1.6  9 years  olson  Update to figfam build code
filter_trunc_and_fs.pl  1.2  9 years  olson  Add SeedUtils::map_to_families for iterating over families.2c files. Make filte...
restore_assignments.pl  1.2  14 years  olson  Add license words.
load_coupling.pl  1.9  14 years  olson  Remove debugging.
Makefile  1.24  9 years  olson  fix R build target. why it works for me and not elsewhere I don't know
assign_synonym_ids_to_sims.pl  1.2  14 years  olson  Add license words.
make_sim_sets.pl  1.3  14 years  olson  Add license words.
make_fasta_btree.pl  1.1  12 years  olson  Utility for creating btree access for fasta files.
get_best_set_of_genes_for_column.pl  1.3  14 years  olson  Add license words.
assign.pl  1.2  14 years  olson  Add license words.
load_coupling_btree.pl  1.1  14 years  olson  BTREE-index versions of these. Experimental still.
svr_status_of_RAST_job.pl  1.4  10 years  olson  add url argument
reformat_dsim_dbs.pl  1.2  14 years  olson  Add license words.
p2p_daemon.pl  1.2  14 years  olson  Add license words.
generate_intergenic_blocks.pl  1.3  14 years  olson  Add license words.
svr.pl  1.2  9 years  olson  add . to include path
package_raw_data_for_transplant.pl  1.2  14 years  olson  Add license words.
to_gids.pl  1.2  14 years  olson  Add license words.
compute_pins.pl  1.4  12 years  olson  undo bogus commit
embl2gff.pl  1.20  14 years  olson  Add license words.
COPYING.TXT  1.1  14 years  olson  add license file
install_rast_batch.pl  1.4  12 years  olson  more fixes
clustal_to_fasta.pl  1.2  14 years  olson  Add license words.
index_fasta.pl  1.2  14 years  olson  Add license words.
assign_to_sets.pl  1.5  14 years  olson  Add license words.
package_assignments.pl  1.8  14 years  olson  Add license words.
index_neighborhoods.pl  1.3  14 years  olson  Add license words.
filter_new_overlaps.pl  1.2  14 years  olson  Add license words.
pull_fasta_entries.pl  1.8  11 years  olson  do not attempt to remap incoming ids
svr_scripts.t  1.2  10 years  olson  updated tests
subtree_of.pl  1.2  14 years  olson  Add license words.
FFB2_get_oligos2.pl  1.3  9 years  olson  Update to figfam build code
bring_system_up_to_date.pl  1.2  14 years  olson  Add license words.
merge_annotations.pl  1.3  14 years  olson  Add license words.
svr_metabolic_reconstruction.pl  1.5  9 years  olson  bah, fix paste error
all_bbhs.pl  1.16  12 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
genomes_of.pl  1.2  14 years  olson  Add license words.
build_access_sets.pl  1.2  14 years  olson  Add license words.
call_genes.pl  1.4  10 years  olson  fix ANNOserver args
report_changes.pl  1.2  14 years  olson  Add license words.
build_sas_distro_from_cvs.pl  1.2  9 years  olson  mods for building myRAST
expand_blast_table.pl  1.2  14 years  olson  Add license words.
compute_changed_ids_for_nrs.pl  1.5  11 years  olson  misc fixes
initialize_ann_and_ev.pl  1.3  12 years  olson  undo bogus commit
make_sim_tab.pl  1.8  13 years  olson  compute_pchs_from_sims.pl
find_neighbors_by_sim.pl  1.4  12 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
check_starts_for_peg_sets.pl  1.5  14 years  olson  Add license words.
is_bacterial.pl  1.2  14 years  olson  Add license words.
make_protein_sets.pl  1.4  14 years  olson  Add license words.
translation_of.pl  1.2  14 years  olson  Add license words.
splitup.pl  1.4  14 years  olson  Add license words.
generate_input_for_auto_assignments.pl  1.2  14 years  olson  Add license words.
check_tbl.pl  1.2  14 years  olson  Add license words.
uninstall.pl  1.2  14 years  olson  Add license words.
register_features_batch.pl  1.2  14 years  olson  Add license words.
FFB2_compare_to_anno3.pl  1.2  9 years  olson  fixes for release names
make_annotations_for_sprout.pl  1.12  14 years  olson  Add license words.
FFB2_genome_group_pipeline.pl  1.1  9 years  olson  New FIGfam merge code.
make_transferable_chunks.pl  1.4  14 years  olson  Add license words.
package_code.pl  1.2  14 years  olson  Add license words.
svr_all_features.pl  1.7  9 years  olson  Deobfuscate the command line logic. Submit requests in chunks so as to not be pa...
map_to_scaffold.pl  1.4  12 years  olson  Actually write out the changed entries.
dump_attributes.pl  1.2  14 years  olson  Add license words.
make_jpg.pl  1.2  14 years  olson  Add license words.
identify_organism.pl  1.2  10 years  olson  changes for new server stuff
make_phob_from_seqs.pl  1.7  14 years  olson  Add license words.
FFB2_make_FF_index.pl  1.2  10 years  olson  Rollup of figfam update fixes
uninstall.sims.pl  1.2  14 years  olson  Add license words.
make_sprout_bbhs.pl  1.2  14 years  olson  Add license words.
check_changes_in_organisms.pl  1.2  14 years  olson  Add license words.
svr_retrieve_RAST_job.pl  1.3  10 years  olson  Misc server fixes
pegs.pl  1.3  14 years  olson  Add license words.
check_all_subsystems.pl  1.11  11 years  olson  Transform the single big select into a prepared statement on per-role select.s
check_sims_syntax.pl  1.3  14 years  olson  Add license words.
auto_assign.pl  1.19  11 years  olson  Add -orgdir option to use FIGV and its indexed sims.
prep_viz.pl  1.2  14 years  olson  Add license words.
fastasize.c  1.3  14 years  olson  Doh, put proper comments in for C code.
extract_data_to_keep.pl  1.5  14 years  olson  Add license words.
mark_nr.pl  1.2  14 years  olson  Add license words.
insert.pl  1.2  14 years  olson  Add license words.
seed_run_task.pl  1.2  13 years  olson  readonly fixes; seed-run-job update to run from input file
install-data.pl  1.8  12 years  olson  fix to dvd data installer
backup_critical_data.pl  1.5  11 years  olson  fix bug that kept subsystems from being backedup
reformat_fasta.pl  1.2  14 years  olson  Add license words.
make_rates.pl  1.2  14 years  olson  Add license words.
import_external_sequences_step1.pl  1.8  14 years  olson  Add license words.
gather_genome_info.pl  1.2  10 years  olson  Add more data gathering
find_genes_based_on_kmers.pl  1.9  9 years  olson  More fixups.
fasta_for_hypo.pl  1.2  14 years  olson  Add license words.
pp.pl  1.3  14 years  olson  Add license words.
FFB2_validate_families.pl  1.1  9 years  olson  Update to FF processing
generate_max_clusters.pl  1.2  14 years  olson  Add license words.
index-pegsyn.pl  1.1  13 years  olson  Missing scripts.
put_directory_in_one_file.pl  1.2  14 years  olson  Add license words.
RunRMA_SIF_format.R  1.1  9 years  olson  SIF-processing run-rma.
expand_sims.pl  1.2  12 years  olson  *** empty log message ***
make_binary.pl  1.2  14 years  olson  Add license words.
build_excel_gene_table.pl  1.3  14 years  olson  Add license words.
reduce_sims.pl  1.12  11 years  olson  fix nasty little bug that drops sims
generate_kernel_css.pl  1.5  14 years  olson  Add license words.
expand_transferred_chunks.pl  1.4  14 years  olson  Add license words.
p2p_sync_from_remote.pl  1.4  14 years  olson  Add license words.
load_bbhs_btree.pl  1.1  14 years  olson  BTREE-index versions of these. Experimental still.
make_calls.pl  1.4  14 years  olson  Add license words.
compute_sim_chunk.pl  1.3  14 years  olson  add working-on-chunk support
add_assertions_of_function.pl  1.38  9 years  olson  add assignment logging, index on org.
convert-blast-to-m8.pl  1.1  11 years  olson  Convert full blast output to -m8 output using Gary's blast parsing code.
FFB2_split_fams_by_size.pl  1.2  9 years  olson  Big round of figfam update changes
make_external_sequence_data.pl  1.2  13 years  olson  remove .pl from invocations
glue_tbl_to_metabolic_reconstruction.pl  1.1  10 years  olson  more anno server fixes, add some missing files
process_new_sims.pl  1.6  13 years  olson  Rollup of various rast-related changes.
assign_synonym_ids_to_nr.pl  1.2  14 years  olson  Add license words.
representative_tree.pl  1.2  14 years  olson  Add license words.
FFB2_get_prots.pl  1.3  10 years  olson  Bunch of figfam generation optimizations.
relevant_PCHs.pl  1.3  14 years  olson  Add license words.
generate_subsys_tables_for_sprout.pl  1.8  14 years  olson  Add license words.
restore_translation_rules.pl  1.2  14 years  olson  Add license words.
build_exemplar_fasta.pl  1.3  14 years  olson  Add license words.
make_occ_counts.pl  1.2  14 years  olson  Add license words.
align_with_clustal.pl  1.8  14 years  olson  Add license words.
fix_ext_funcs.pl  1.2  14 years  olson  Add license words.
index_translations_MD5.pl  1.4  11 years  olson  revert changes
CheckCELfiles.R  1.1  10 years  olson  R script to find chip name from CEL files
find_genes_in_families.pl  1.22  10 years  olson  Switch to FFs and FF instead of FigFams and FigFam
FFB2_build_updated_FF.pl  1.23  9 years  olson  Update to figfam build code
import_subsystems.pl  1.22  14 years  olson  Add license words.
run_rabbit_daemon_set.pl  1.3  9 years  olson  remove debug
check_fasta_for_dups.pl  1.1  13 years  olson  Missing scripts.
fig_xmlrpc_server.pl  1.5  14 years  olson  Add license words.
install_code.pl  1.2  14 years  olson  Add license words.
load_local_maps.pl  1.3  14 years  olson  Add license words.
build_protein_families.pl  1.5  14 years  olson  Add license words.
update_sims2.pl  1.6  9 years  olson  updated code
generate_pin_caches.pl  1.5  14 years  olson  Add license words.
list_genomes.pl  1.2  14 years  olson  Add license words.
svr_ACH.t  1.1  10 years  olson  new tests
peg_to_name.pl  1.4  14 years  olson  Add license words.
blastP.pl  1.1  10 years  olson  Switch to using assign_functions_to_prot_set in assign_using_kmers.pl. Add blast...
distribute_attributes.pl  1.11  14 years  olson  Add license words.
rationalize_blast.pl  1.3  14 years  olson  Add license words.
assign_to_dna_using_kmers.pl  1.5  10 years  olson  more anno server fixes, add some missing files
load_chromosomal_clusters.pl  1.2  14 years  olson  Add license words.
FFB2_install_kmers.pl  1.2  9 years  olson  Update to FF processing
ensure_genome_registration.pl  1.1  13 years  olson  generate feature registration stuff
function_of.pl  1.5  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
salvage_subsystem_rows.pl  1.6  14 years  overbeek  fixes to salvage code
ma_pipeline.pl  1.15  9 years  overbeek  get rid of RMA Key
possible_frameshifts.pl  1.1  13 years  overbeek  update possible_frameshifts
order_figfams.pl  1.1  14 years  overbeek  order_figfams
blastn_chunks.pl  1.3  13 years  overbeek  initial, undebugged version of edit_feature.cgi
add_to_subsystems.pl  1.1  13 years  overbeek  add add_to_subsystems
indirect_functional_coupling.pl  1.5  13 years  overbeek  indirect functional coupling should not be from a PEG to itself
make_sims_and_fc_data.pl  1.1  11 years  overbeek  add wrapper to building partition-based similarity and fc data
estimated_fabric.pl  1.1  11 years  overbeek  code for processing fabrics and population estimates
make_partition_repsW.pl  1.1  11 years  overbeek  try
svr_find_clusters_relevant_to_reaction.pl  1.5  9 years  overbeek  handle case in which no roles are needed
make_scored_instances.pl  1.4  11 years  overbeek  minor changes
bring_tree_up_to_ali.pl  1.5  13 years  overbeek  debugged version of bring_tree_up_to_ali
uproot.pl  1.1  13 years  overbeek  add uproot
svr_representative_sequences.pl  1.1  9 years  overbeek  keep representative_sequences, but make it a shadow of the new svr_representativ...
get_coupling_values.pl  1.3  9 years  overbeek  get rid of extraneous routine
nmpdr2gff.pl  1.1  14 years  overbeek  RAE: Changes to gff3 files for NMPDR and adding nmpdr2gff for creating the files...
align_seqs.pl  1.1  13 years  overbeek  add utilities for computing alignments
make_peg_maps.pl  1.3  14 years  overbeek  minor fixes
test_placement.pl  1.1  12 years  overbeek  redone FIGfam stuff
order_seqs_on_length.pl  1.1  13 years  overbeek  add utilities for computing alignments
svr_neighboring_reactions.pl  1.2  9 years  overbeek  minor fixes
flattened_to_fasta.pl  1.1  14 years  overbeek  add some minor utilities to flatten/unflatten fasta files
compare_two_sets_of_calls.pl  1.3  11 years  overbeek  stuff for gene calling
compute_atomic_regulons_for_dir.pl  1.2  9 years  overbeek  loosen threshhold of mismatches
load_go.pl  1.2  13 years  overbeek  put in the fr2go stuff
svr_functionally_coupled.pl  1.2  9 years  overbeek  add cutoffs
filter_on_known.pl  1.1  10 years  overbeek  filter pegs with no raw data
check_subs_and_split_warnings.pl  1.3  12 years  overbeek  minor fix to handle deleted subsystems
flatten_fasta.pl  1.1  14 years  overbeek  add some minor utilities to flatten/unflatten fasta files
connections_between.pl  1.8  11 years  overbeek  fixes to making close strain data
cluster_objects.pl  1.5  9 years  overbeek  require connections to begin each line
svr_sketch_tree.pl  1.1  9 years  overbeek  slightly modified version of the older sketch_tree
update_nr_cycle.pl  1.6  14 years  overbeek  load ext org table on update_nr_cycle
same_figfam.pl  1.2  12 years  overbeek  handle bad input in same_figfam
sims_between.pl  1.7  12 years  overbeek  updates on close connections
close_connections.pl  1.2  12 years  overbeek  add strip comments argument on function_of
uni_lit_to_dlits.pl  1.1  12 years  overbeek  dlit support
svr_by_taxonomy.pl  1.3  9 years  overbeek  fix parameter passing
reps_and_close.pl  1.2  13 years  overbeek  add make_trimmed_alignment_from_ids
split_assignments_based_on_subsystems.pl  1.1  14 years  overbeek  next version of the STAG code
make_initial_partition_scores.pl  1.1  11 years  overbeek  additions to support partitioning of sims
filter_tbl_overlaps.pl  1.10  14 years  overbeek  set up find_neighbors to handle existing genomes
diff_tbls.pl  1.1  14 years  overbeek  Computes difference betwween two tbl files. -- /gdp
generate_comparisons.pl  1.1  11 years  overbeek  stuff for gene calling
check_subsystems.pl  1.7  13 years  overbeek  strip comments on functions for subsystem checking
compute_atomic_regulons.pl  1.2  9 years  overbeek  compute atomic regulons only for new data
purge_fasta.pl  1.1  14 years  overbeek  Removes duplicate entries from fasta file. -- /gdp
fast_blastp.pl  1.1  12 years  overbeek  fast_blastp is a tool to support rapid similarity estimates using FIGfam partiti...
svr_tips_of_tree.pl  1.2  9 years  overbeek  add correspondence translation
score_ifcs_mcauliffe.pl  1.2  13 years  overbeek  RAE: correcting indirect functional coupling score
svr_get_coupling_data.pl  1.2  9 years  overbeek  must have -d
run_gene_calling_scripts.pl  1.3  11 years  overbeek  fix first arg on call to mark_picked_genes
generate_picked.pl  1.1  11 years  overbeek  stuff for gene calling
svr_summarize_protein_families.pl  1.2  9 years  overbeek  minor changes
seed2pir.pl  1.3  14 years  overbeek  RAE: moving PIRSF to links
svr_is_hypo.pl  1.3  9 years  overbeek  minor fixes
svr_fc_figfams.pl  1.3  9 years  overbeek  sort by score
check_for_possible_mobile_elements.pl  1.1  12 years  overbeek  add code to search for mobile elements
remove_clustered_pchs.pl  1.10  13 years  overbeek  fix rfemove_clustered_PCHs to count correctly
svr_subsystem_roles.pl  1.2  9 years  overbeek  allow ss from stdin
make_close_strain_family_tabs.pl  1.2  14 years  overbeek  fixes to wseekly statistics
get_figfam_funcs.pl  1.1  13 years  overbeek  add install_anticipated_functions and some FIGfam tracking stuff
make_subsys_based_families.pl  1.14  11 years  overbeek  do not use genomes with variants beginning with an asterisk in forming FIGfams b...
svr_assign_to_dna_using_figfams.pl  1.15  9 years  overbeek  default kmer=8
svr_find_regulatory_proteins.pl  1.1  9 years  overbeek  a simple tool to find potential regulatory proteins
svr_make_pan_genome_prot_families.pl  1.7  9 years  overbeek  parallelize computation of correspondnece tables
svr_role_to_pegs.pl  1.3  9 years  overbeek  mispelled genome with bad consequences
split_and_trim_sequences.pl  1.14  13 years  overbeek  fix problem when repeats occur
mark_picked_genes.pl  1.2  11 years  overbeek  fix order of arguments
find_bad_conflicts.pl  1.1  14 years  overbeek  fixes to wseekly statistics
FFB2_load_oligo_index.pl  1.1  10 years  overbeek  new scripts for updating FIGfams and Kmer tables
generate_GO_attributes.pl  1.1  13 years  overbeek  add GO attribute genertation
make_sim_part_data.pl  1.1  11 years  overbeek  add command to build similarity partitions
indirect_functional_coupling_mcauliffe.pl  1.5  13 years  overbeek  indirect functional coupling should not be from a PEG to itself
compute_ev_code_attributes.pl  1.2  12 years  overbeek  do not include cluster-based subsystems in forming evidence codes
merge_gene_sets.pl  1.1  10 years  overbeek  code from Hope
svr_corresponding_genes2.pl  1.3  9 years  overbeek  updates for correspondence maps
svr_possible_joins.pl  1.1  9 years  overbeek  tools to try to bridge contigs
merge_families.pl  1.3  12 years  overbeek  add strip comments argument on function_of
get_translations.pl  1.3  14 years  overbeek  get_translations can take PEG ids from STDIN
svr_blast.pl  1.1  9 years  overbeek  interface to blast
potentially_missed_assignments.pl  1.1  13 years  overbeek  add potentially_missed_assignments
svr_reroot_tree.pl  1.3  9 years  overbeek  fix typo
make_neigh_joining_tree.pl  1.8  13 years  overbeek  debugged version of bring_tree_up_to_ali
svr_fasta.pl  1.14  9 years  overbeek  wrap the seq into 60-char lines
get_rna_features_for_calling_genes.pl  1.2  11 years  overbeek  get rid of proteins
tips_of.pl  1.3  13 years  overbeek  add insert_prot_into_tree, a new way to insert proteins into a tree
svr_genome_functions.pl  1.3  9 years  overbeek  sort by feature id
svr_coregulated_by_correspondence.pl  1.6  9 years  overbeek  handle peg related to peg
make_proposed_assignments_for_consistency.pl  1.4  14 years  overbeek  fixes to wseekly statistics
same_subsys.pl  1.1  14 years  overbeek  fixes to extract_genomes
export_similarity_request.pl  1.3  14 years  overbeek  minor fixes to assignment for close strains
EcoliRMA.R  1.2  10 years  overbeek  from Matt
check_and_extend_all_subsystems.pl  1.7  13 years  overbeek  fix call to rapid_subsystem_extension in check_and_extend_all_subsystems
build_partition_index.pl  1.1  12 years  overbeek  return empty list of failure to open FIFfam
generate_dlit_ev_codes.pl  1.5  12 years  overbeek  switching to new ilidt/dlit stuff
rep_genomes.pl  1.1  13 years  overbeek  fixes to representative tree generation and added rep_genomes
find_subsys.pl  1.3  12 years  overbeek  allow loose matching in rapid_propagation
best_tree_using_proml_on_cluster.pl  1.1  13 years  overbeek  add best_tree_using_proml_on_cluster
svr_cut_domain.pl  1.1  9 years  overbeek  cut domains from sequences
cluster_exp.pl  1.1  9 years  overbeek  cluster experiments into states
svr_update_corr_maps.pl  1.2  9 years  overbeek  minor fix
update_fr2go.pl  1.1  13 years  overbeek  put in the fr2go stuff
wb.pl  1.1  10 years  overbeek  workbench for alignments and trees
load_locks.pl  1.1  13 years  overbeek  introduce locks on features to block assignments
check_peg_placement.pl  1.1  12 years  overbeek  redone FIGfam stuff
make_coreg_conjectures_based_on_subsys.pl  1.6  9 years  overbeek  allow working from estiomates of SS
get_subsystem_properties.pl  1.1  12 years  overbeek  minor modifications to get subsystems statistics
evaluate_quality_of_trees.pl  1.4  13 years  overbeek  debugged version of bring_tree_up_to_ali
assign_to_close_strains.pl  1.10  14 years  overbeek  fixes to Assignments.pm
generate_ilit_ev_codes.pl  1.4  12 years  overbeek  code relating to dlit/ilit maintenance
initialize_alignments_for_subsystems.pl  1.2  14 years  overbeek  fixes to extract_genomes, salvage_subsystem_rows and initialize_alignments_for_s...
load_ACH_resolution_DB.pl  1.4  12 years  overbeek  fixes to quotemeta characters in loading comments
extract_fasta_idmap.pl  1.1  14 years  overbeek  RAE: Adding FigKernelScripts/extract_fasta_idmap.pl
rebuild_global_chromosomal_clusters.pl  1.2  12 years  overbeek  version of rebuild_global_chromosomal_clusters that works
svr_oligomer_similarity.pl  1.1  9 years  overbeek  compute oligo similarities
partition_prots.pl  1.4  11 years  overbeek  check to make sure sims are working
make_kegg_files.pl  1.5  13 years  overbeek  Update parsing of NAME field to reflect change in source file. -- /gdp
svr_scanN.pl  1.1  9 years  overbeek  scanning utilities
insert_into_a_tree.pl  1.5  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
make_FigFamsData.pl  1.4  14 years  overbeek  order generated FIGfams
iedb.pl  1.10  13 years  overbeek  RAE: bugger, correcting the array dereferencing
curator_of.pl  1.1  14 years  overbeek  minor fixes to assignment for close strains
make_close_strain_data.pl  1.14  11 years  overbeek  fixes to making close strain data
fabric_vec.pl  1.1  11 years  overbeek  add ability to make fabric vecs
update_OTUs.pl  1.5  9 years  overbeek  fix OTU update to use gary olsen sequence grouping script
svr_add_lengths_to_blast.pl  1.1  9 years  overbeek   simple utility to add sequence lengths to m8 blast output
make_uniprot_corr.pl  1.2  12 years  overbeek  build uniprot correspondence
split_clean_unclean_families.pl  1.4  14 years  overbeek  fixes for splitting families into clean/unclean
runclustalw.pl  1.4  13 years  overbeek  add computation of alignments to building FIGFAMS
make_figfams.pl  1.3  13 years  overbeek  families.2c should get current function - not family function
trim_sequences.pl  1.11  10 years  overbeek  fixes bug in handling multidomain prots
ShewanellaRMA.R  1.1  10 years  overbeek  code from Hope
pegs_in_subsystem.pl  1.6  11 years  overbeek  check for aux roles
svr_find_hypos_for_cluster.pl  1.1  9 years  overbeek  find hypotheticals associated with clusters
bielefeld_tarfile_to_seed.pl  1.7  13 years  overbeek  Tweaked usage msg. -- /gdp
score_ifcs.pl  1.4  13 years  overbeek  RAE: More direct and indirect functional coupling scores
load_pirsf.pl  1.14  14 years  overbeek  RAE: correcting load_pirsf not recognizing a firewall
make_parallel_proml_run.pl  1.2  13 years  overbeek  add rates to phylogeny stuff
svr_corresponding_genes.pl  1.24  9 years  overbeek  fix command line arguments
filter_and_merge_gene_sets.pl  1.2  9 years  overbeek  merge is better
svr_big_repeats.pl  1.1  9 years  overbeek  tool to search for large repeats
pop_vec.pl  1.1  11 years  overbeek  code for processing fabrics and population estimates
package_subsystems.pl  1.5  14 years  overbeek  fixes to deleted_features, replace_features_with, etc
make_ma_html.pl  1.2  9 years  overbeek  minor fixes
conditionally_assign.pl  1.5  11 years  overbeek  get rid of warning and update conditionally_assign
svr_summarize_MG_output.pl  1.4  10 years  overbeek  extend the number of digits in the fraction of the total
functionally_coupled.pl  1.7  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
svr_otus.pl  1.3  9 years  overbeek  minor fixes
load_protein_families.pl  1.9  14 years  overbeek  RAE: extending protein families
new_versions_of_features.pl  1.1  14 years  overbeek  add new_versions_of_features
svr_all_models.pl  1.2  9 years  overbeek  keep only Seed models
svr_md5_of_prot.pl  1.1  9 years  overbeek  get md5s for pegs
trimmed_kernel_alignment.pl  1.1  13 years  overbeek  add last round of phylogeny tools
ma_pipeline_shewanella.pl  1.6  10 years  overbeek  fixes to pipeline
filter_figfams.pl  1.2  13 years  overbeek  add computation of alignments to building FIGFAMS
track_figfams.pl  1.2  13 years  overbeek  get rid of diagnostics in track_figfams
subsys_info.pl  1.1  12 years  overbeek  subsys_info is subsystem information for Verionika
score_dfcs_mcauliffe.pl  1.5  13 years  overbeek  limit decimal positions in score
run_find_subsys_against_all_genomes.pl  1.2  12 years  overbeek  updates to computation of VCs
compare_tbls.pl  1.5  13 years  overbeek  Minor change to output. -- /gdp
svr_scanP.pl  1.2  9 years  overbeek  add a little documentation
svr_inherit_aliases.pl  1.1  9 years  overbeek  inherit aliases
filter_overlaps.pl  1.5  13 years  overbeek  Added some more diagnosting lines. -- /gdp
svr_call_pegs.pl  1.2  9 years  overbeek  fix POD stuff
svr_missing_roles.pl  1.2  9 years  overbeek  added -g genome
update_taxonomies.pl  1.8  13 years  overbeek  set longer gap between accessing NCBI
update_SSU_rRNAs.pl  1.1  11 years  overbeek  update of SSUs
are_close.pl  1.1  14 years  overbeek  fixes to extract_genomes
svr_keep_only.pl  1.1  9 years  overbeek  support filtering on function or role
make_trimmed_alignment_from_ids.pl  1.13  12 years  overbeek  return empty list of failure to open FIFfam
compute_pc.pl  1.1  10 years  overbeek  code from Hope
svr_ids_to_figfams.pl  1.8  9 years  overbeek  fixes to documentation
rel2tabs.pl  1.1  14 years  overbeek  minor tools
purge_tbl.pl  1.1  14 years  overbeek  Removes duplicate entries from tbl file. -- /gdp
to_structured_english.pl  1.1  12 years  overbeek  add routine to build structured english rendering of evidence codes
make_fam_tabs.pl  1.5  14 years  overbeek  RAE: Protein Families interface and construction
score_dfcs.pl  1.3  13 years  overbeek  RAE: removing the header that should not be in the source
pick_feature_set.pl  1.1  11 years  overbeek  choose genes from candidates
make_assertions_from_uploads.pl  1.3  11 years  overbeek  get rid of debugging message
trim_alignment.pl  1.2  13 years  overbeek  minor fixes
compute_potential_fusions.pl  1.12  14 years  overbeek  fix to fusions
delete_all_attribute_files.pl  1.2  14 years  overbeek  RAE: New delete attribute files to remove all files. maybe this will work
ma_pipeline_ecoli.pl  1.2  10 years  overbeek  pipeline for Ecoli
make_timestamps.pl  1.4  13 years  overbeek  add initial version of FIGO.pm - OO services
svr_split_fams.pl  1.1  9 years  overbeek  minor changes
fasta_size.pl  1.1  11 years  overbeek  add fasta_size
bayes_expected_start_scores.pl  1.3  13 years  overbeek  Added comments to expalin logic. -- gdp
load_close.pl  1.9  13 years  overbeek  tighten length constraints for figfam matching
ali_tree.pl  1.4  12 years  overbeek  add strip comments argument on function_of
export_ACH_resolution_DB.pl  1.2  12 years  overbeek  fixes relating to comments
extract_genomes.pl  1.38  14 years  overbeek  changes to support dynamic sims and updates
svr_cluster_pegs.pl  1.1  9 years  overbeek  two small utilities
make_partition_reps.pl  1.1  11 years  overbeek  try
myjoin.pl  1.1  14 years  overbeek  fix building FigFamData
split_sequences_into_sets.pl  1.5  10 years  overbeek  handle asym connections
build_all_prok_seqs.pl  1.1  10 years  overbeek  get all protein sequences for complete prokaryotic genomes
FFB2_get_prot_gs_oligos.pl  1.1  10 years  overbeek  new scripts for updating FIGfams and Kmer tables
split_by_genome.pl  1.1  13 years  overbeek  split_by_genome can be used to split a score or BBH file
read_write_excel.pl  1.1  14 years  overbeek  RAE: Initial release of a simple script to read and write excel files to allow e...
pegs_in_subsystems.pl  1.8  10 years  overbeek  fix documentation
check_for_new_genomes.pl  1.3  11 years  overbeek  print stats as you go
sims_all.pl  1.6  11 years  overbeek  remove paralogs before computing conections
svr_fig_id_corr.pl  1.4  10 years  overbeek  add -precise option
svr_with_close_blast_hits.pl  1.1  9 years  overbeek  a utility to find close hits
clustered_hypotheticals.pl  1.2  10 years  overbeek  major rewrite
predicted_vs_actual.pl  1.1  11 years  overbeek  basic metagenomic tools
find_poss_fs.pl  1.1  12 years  overbeek  add code to fix frameshifts in a genome
salvage_master_annotations.pl  1.3  14 years  overbeek  fixes to salvage code
format_partition_dbs.pl  1.2  11 years  overbeek  try
compareMR.pl  1.1  13 years  overbeek  basic stuff for comparing metabolic reconstructions
direct_functional_coupling.pl  1.4  13 years  overbeek  tighten length constraints for figfam matching
svr_rep_seqs.pl  1.2  10 years  overbeek  add SAS component
ma.cgi  1.1  10 years  overbeek  added massaging and voting
representative_sequences.pl  1.6  9 years  overbeek  keep representative_sequences, but make it a shadow of the new svr_representativ...
aclh.pl  1.11  12 years  paarmann  added new parameter to dump contribs
cache_comparison_data.pl  1.11  11 years  paczian  fixed load order of function files in RAST vs SEED organisms
svr_subsystem_genomes.pl  1.1  9 years  parrello  Discrimination functions support scripts.
exclude_genomes.pl  1.3  12 years  parrello  Fixed a POD error.
svr_reaction_description.pl  1.3  9 years  parrello  Added -f flag.
import_similarity_bundle.pl  1.3  12 years  parrello  Fixed a POD error.
svr_contigs_in_genome.pl  1.3  9 years  parrello  Added support for specifying input IDs on the command line.
svr_close_genomes.pl  1.1  9 years  parrello  More server script stuff. Thought I'd already installed these last week...
svr_expressed_genes_in_range.pl  1.1  9 years  parrello  Added for looking at genes that are never or always expressed.
svr_mapped_genomes.pl  1.3  9 years  parrello  Added "roles_to_subsys", sped up "figfams_to_ids", fixed pod for "mapped_genomes...
svr_discriminating_functions.pl  1.3  9 years  parrello  Discrimination functions support scripts.
svr_all_subsystems.pl  1.9  10 years  parrello  Fixed POD errors. Added examples.
svr_figfam_functions.pl  1.2  9 years  parrello  Added option to get all the FIGfams.
svr_roles_to_subsys.pl  1.1  9 years  parrello  Added "roles_to_subsys", sped up "figfams_to_ids", fixed pod for "mapped_genomes...
svr_summarize_contigs.pl  1.2  9 years  parrello  New script, some documentation fixes.
svr_function_of.pl  1.11  9 years  parrello  Converted to use "GetBatch" to flow-control the requests.
svr_similar_to.pl  1.2  10 years  parrello  Fixed POD errors.
svr_reactions_to_roles.pl  1.1  9 years  parrello  New chemistry-based scripts.
analyze_loose_sets.pl  1.3  9 years  parrello  Added CSV output that can be used to generate a spreadsheet of recommended funct...
svr_dna_seq.pl  1.2  9 years  parrello  More server script stuff.
svr_gene_data.pl  1.3  9 years  parrello  First round of script updates & additions for tutorial.
make_close.pl  1.7  13 years  parrello  Fixed obsolete form of boundaries_of.
svr_determine_sets_of_related_contigs.pl  1.4  10 years  parrello  Documentation fixes.
svr_all_reactions.pl  1.1  9 years  parrello  New chemistry-based scripts.
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_pegs_in_subsystems.pl  1.7  9 years  parrello  Fixed to process 10 subsystems at a time, reducing the chances of a timeout.
svr_ach_lookup.pl  1.10  9 years  parrello  More server script stuff. Thought I'd already installed these last week...
svr_reactions_in_model.pl  1.1  9 years  parrello  New script for Ross.
svr_location_of.pl  1.1  9 years  parrello  Added due to seminar user request.
svr_ss_classes.pl  1.1  9 years  parrello  Added to get classification data for subsystems.
server_paper_figure2.pl  1.2  10 years  parrello  Removed genetic codes so program fits better on a page.
build_sets_from_clusters.pl  1.2  9 years  parrello  Minor fixes for debugging.
server_paper_example6.pl  1.3  10 years  parrello  Fixed for server paper.
run_glimmer3.pl  1.14  10 years  parrello  Added "-verbose" option so tracing can be turned on from the servers.
get_pairs.pl  1.1  11 years  parrello  New script to find certain functional roles close together.
LigandCleanup.pl  1.2  12 years  parrello  Removed obsolete use clases.
svr_fids_for_md5.pl  1.1  9 years  parrello  New method to return FIG IDs for a protein given its MD5.
svr_in_runs.pl  1.5  10 years  parrello  Fixed POD errors. Added examples.
svr_intergenic_regions.pl  1.1  9 years  parrello  New script to find intergenic regions.
NMPDRAnalysis.pl  1.5  12 years  parrello  Removed obsolete use clauses.
svr_call_rnas.pl  1.1  9 years  parrello  More server scripts.
svr_closest_genes.pl  1.1  9 years  parrello  More server script stuff.
PickGeneBoundariesTest.pl  1.1  12 years  parrello  Test script for backfill.
svr_atomic_regulons.pl  1.1  9 years  parrello  Added to allow retrieval of pegs in atomic regulons.
EmergencyMapFlipper.pl  1.2  10 years  parrello  *** empty log message ***
server_paper_example4.pl  1.3  10 years  parrello  Fixed to use the correct servers.
svr_aliases_to_pegs.pl  1.1  9 years  parrello  New script for Ross
svr_coupled_reactions.pl  1.1  9 years  parrello  New chemistry-based scripts.
OneShotAttributeAdder.pl  1.2  12 years  parrello  Removed obsolete use clauses.
svr_submit_correspondences.pl  1.1  9 years  parrello  First round of script updates & additions for tutorial.
TransactFeatures.pl  1.20  12 years  parrello  Removed obsolete use clause.
svr_subsystem_genome_data.pl  1.1  9 years  parrello  More server scripts.
TestLocations.pl  1.8  12 years  parrello  Converted to use new name for Contrain method.
get_ev_codes.pl  1.15  11 years  parrello  Updated comments to mention the replacement scripts.
SpanishInquisition.pl  1.1  12 years  parrello  Added for testing the Confess method.
backup_subsystems.pl  1.3  12 years  parrello  Fixed a POD error.
svr_all_experiments.pl  1.1  9 years  parrello  Added to get experiments for each genome.
svr_fasta_to_md5.pl  1.1  9 years  parrello  New script for computing MD5s from FASTA protein sequences.
svr_exp_genomes.pl  1.1  9 years  parrello  New script to list expression-data genomes.
svr_genome_statistics.pl  1.2  9 years  parrello  Added genome name to the POD.
load_abstract_coupling.pl  1.3  14 years  parrello  Changed to use a single-character delimiter (for compatability with PostGRES).
map_pegs.pl  1.3  13 years  parrello  Fixed obsolete form of boundaries_of.
svr_all_figfams.pl  1.2  10 years  parrello  Documentation fixes.
WikiMaker.pl  1.6  11 years  parrello  Added more trace messages.
ev_code_cron.pl  1.16  11 years  parrello  Updated comments to mention the replacement scripts.
server_paper_example1.pl  1.12  10 years  parrello  Documentation fix for server paper.
svr_neighbors_of.pl  1.3  10 years  parrello  Fixed POD errors. Added examples.
svr_neighborhood_of_role.pl  1.3  9 years  parrello  Converted to use chemistry data instead of the models.
ListLits.pl  1.1  11 years  parrello  New script to count literature references for NMPDR.
corr_build_connections.pl  1.1  9 years  parrello  New stuff for Salmonella sets.
Tracer.pl  1.1  11 years  parrello  New script used to route STDERR messages to the trace log.
svr_distinct_otus.pl  1.4  9 years  parrello  Added support for specifying input IDs on the command line.
svr_corr_by_exp.pl  1.5  9 years  parrello  Changed to batch the input instead of slurping it.
load_md5_alignment.pl  1.1  9 years  parrello  New script to load alignments into the PUBSEED server.
form_clusters.pl  1.2  10 years  parrello  Final Server updates.
svr_all_genomes.pl  1.2  9 years  parrello  First round of script updates & additions for tutorial.
svr_figfam_fasta.pl  1.5  9 years  parrello  More server script stuff. Thought I'd already installed these last week...
svr_subsystem_spreadsheet.pl  1.1  9 years  parrello  subsystem download scripts.
svr_members_of_otu.pl  1.3  9 years  parrello  Added support for specifying input IDs on the command line.
svr_upstream.pl  1.8  9 years  parrello  More server script stuff. Thought I'd already installed these last week...
trace.pl  1.3  12 years  parrello  Fixed so that the destination is not case-sensitive.
pubbed_fids.pl  1.1  10 years  parrello  New script to find features with publications attached.
convert_tbl_files.pl  1.1  9 years  parrello  New script for fancy tbl file conversion.
svr_roles_to_reactions.pl  1.1  9 years  parrello  New script for reactions of roles.
Packager.pl  1.7  12 years  parrello  Changed POD format for better compatability with Wiki.
genomes_with_essentiality_data.pl  1.1  13 years  redwards  Adding tools to handle essentiality data for Sveta
export_phage_data.pl  1.2  9 years  redwards  updating date
fix_invalid_fasta.pl  1.1  12 years  redwards  Initial release of programs to check and fix valid fasta format
add_attributes_from_file.pl  1.1  13 years  redwards  just a simple attribute loader
difference_between_two_databases.pl  1.1  11 years  redwards  code for generating the delta between two databases
flatten_attribute_files.pl  1.2  9 years  redwards  working on all subdirectories, not just a set of them
genbank2fasta.pl  1.2  10 years  redwards  correcting ORIGIN regexp
seed2gff.pl  1.36  12 years  redwards  getting rid of need for strain info
load_ss_classification.pl  1.1  11 years  redwards  adding ss classification methods
compute_translation_MD5.c  1.3  9 years  redwards  ignoring stops
load_attributes.pl  1.46  9 years  redwards  changing the attribute of the genome table
gff_statistics.pl  1.1  13 years  redwards  releasing gff statistics
blastp_pseq.pl  1.6  10 years  redwards  adding a default cutoff
adjacent.pl  1.3  12 years  redwards  changing chop to chomp
seed2genbank.pl  1.5  10 years  redwards  fixing major bug that was removing all stop positions
rapid_subsystem_inference.pl  1.17  9 years  redwards  removing zero length keys
validate_fasta.pl  1.1  12 years  redwards  Initial release of programs to check and fix valid fasta format
summarize_taxonomy_by_blast.pl  1.9  12 years  redwards  removing fatal error if 0 or 1 hits
index_translation_files.c  1.8  9 years  redwards  ignoring stops
svr_just_ends.pl  1.3  9 years  redwards  increasing min length to 2000 so that you have two ends!
gff2tab.pl  1.5  13 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
check_sims_basic.pl  1.8  13 years  redwards  using is_environmental instead of seven 9s
blast2gff.pl  1.23  9 years  redwards  adding an option for gziped files
pubmed_gene2peg.pl  1.2  13 years  redwards  making sure gene id is right
mark_genome_as_phage.pl  1.1  9 years  redwards  two phage specific scripts
dp.pl  1.4  10 years  redwards  editing header info
index_contigs.pl  1.12  9 years  redwards  not reopening a file twice!
correct_gff_missing_contigs.pl  1.5  12 years  redwards  correcting a weird error
get_ss_connections.pl  1.12  10 years  redwards  only call if not in a ss
dump_ss_classification.pl  1.1  11 years  redwards  adding ss classification methods
check_consistency_of_sample.pl  1.7  10 years  redwards  correcting looping through parts of the genomes
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
gff2seed.pl  1.29  11 years  redwards  removing check for refseq ids
fig.pl  1.155  9 years  redwards  adding a method to list all phages
build_alignments_from_spreadsheet.pl  1.7  13 years  redwards  using is_environmental
make_ncbi_files.pl  1.4  13 years  wilke  changed check for existing directories
update_lineage.pl  1.3  12 years  wilke  draft version to update FIG taxonomy entries
make_sp_uni_files.pl  1.4  13 years  wilke  changed check for input and output directory the directories may exists, so don'...
aclh_reload_contrib.pl  1.2  11 years  wilke  added db handle in ach call
get_id_mapping_for_list_of_IDs.pl  1.1  11 years  wilke  Draft version for id mapping
get_synonyms_from_ach_for_id.pl  1.2  12 years  wilke  *** empty log message ***
get_genomes_from_ncbi.pl  1.1  10 years  wilke  *** empty log message ***

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