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Index of /FigKernelScripts

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File Rev. Age Author Last log entry
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connect_PDB_to_FIGfams_worker.pl  1.1  12 years  arodri7  update changes
get_NCBI_genome_attributes.pl  1.1  12 years  arodri7  get_NCBI_genome_attributes searches the NCBI internet sites for genome attribute...
build_new_figfam_release.pl  1.4  12 years  arodri7  made default procedure the ross hack for new families
make_figfam_tree.pl  1.1  12 years  arodri7  update changes
propagate_subsys_changes_to_figfams.pl  1.9  12 years  arodri7  update changes
figfam_quality_control.pl  1.7  12 years  arodri7  update changes
install_partitions.pl  1.3  12 years  arodri7  update changes
connect_PDB_to_FIGfams.pl  1.1  12 years  arodri7  update changes
test_figfam_peg.pl  1.6  12 years  arodri7  update changes
figfam_subsystems.pl  1.1  12 years  arodri7  update changes
figfam_size_distribution.pl  1.1  12 years  arodri7  update changes
assign_using_ff.pl  1.3  12 years  arodri7  update changes
initialize_figfams.pl  1.7  12 years  arodri7  update changes
make_figfam_tree_worker.pl  1.1  12 years  arodri7  update changes
submit_ff_test.pl  1.4  12 years  arodri7  update changes
update_FIGfams.pl  1.10  12 years  arodri7  update 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 ***
createTIGRfamSrc.pl  1.1  12 years  bartels  *** empty log message ***
set_not_private.pl  1.1  11 years  bartels  *** empty log message ***
compare_scenarios.pl  1.4  12 years  dejongh  Hope College updates
load_kegg.pl  1.9  12 years  dejongh  *** empty log message ***
check_hope_info.pl  1.3  12 years  dejongh  hope script
add_structured_english.pl  1.4  12 years  disz  Added escape arg to structured engkish
show_structured_english.pl  1.1  12 years  disz  Ross's code to generate annotations for NCBI
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).
find_missing_lib_inputs.pl  1.5  12 years  formsma  Updated error statements. Added compound name printing. - Kevin
run_model_generation.pl  1.16  12 years  formsma  Added timestamp in GMT to the readme that is generated - Kevin
find_essential_reactions.pl  1.2  12 years  formsma  Fixed incorrect filehandle. Tested Good - Kevin
make_SBML_model.pl  1.5  12 years  formsma  Added reaction ATPSYN for manual since KEGG doesn't have it - Kevin
run_model_generation_all.pl  1.1  12 years  formsma  This script will generate models for all complete genomes in the seed. - Kevin
find_model_information.pl  1.6  12 years  formsma  Changed logic on input prediction for dealing with biomass compounds - Kevin
predict_scenarios.pl  1.2  13 years  formsma  Added code to automatically run 'run_scenarios All' if it hasn't been run. These...
make_MPS_model.pl  1.6  12 years  formsma  Updated some logic for the sink reactions. Fixes flux issues - Kevin
run_scenarios.pl  1.3  13 years  formsma  Updated error statements to be correct - Kevin
remove_embedded_pegs.pl  1.17  12 years  gdpusch  Added setting of VERBOSE from metafile. -- /gdp
reformat_contigs.pl  1.16  11 years  gdpusch  Modified to split on runs of ambigs, not just N or X. -- /gdp
build_figfam_pssm_db.pl  1.2  13 years  gdpusch  Major modifications to &load_family_ids()
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  1.9  12 years  gdpusch  Added support for multi-exon locations. -- /gdp
add_sim_data_for_start_predictions.pl  1.8  12 years  gdpusch  Added FIGV support. -- /gdp
find_genes_based_on_neighbors.pl  1.22  12 years  gdpusch  Final clean-up. -- /gdp
sequence_length_histogram.pl  1.4  12 years  gdpusch  Rewrote counting of DNA characters (-get_dna option). -- /gdp
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
run_glimmer3.pl  1.9  11 years  gdpusch  Fixed neglected linear topology swicth. -- /gdp
verify_genome_directory.pl  1.36  11 years  gdpusch  Augmented genetic code table to translate ambiguous codons that _could_ be STOPs...
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
make_peg_map_from_tbl.pl  1.2  12 years  gdpusch  Removed hard-coded regexps that failed to handle multi-exon loci. -- /gdp
to_genbank.pl  1.4  12 years  gdpusch  Added support for multiple contig files. -- /gdp
find_neighbors_using_figfams.pl  1.8  12 years  gdpusch  Added comments, divide-by-zero protection, and removed an ill-thought-out hand-o...
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  1.20  12 years  gdpusch  No longer complains about split loci. -- /gdp
add_start_data_for_start_predictions.pl  1.4  12 years  gdpusch  Added FIGV support. -- /gdp
find_gaps.pl  1.8  12 years  gdpusch  Fixed error in lower boundary constraint. -- /gdp
get_potential_starts_for_start_predictions.pl  1.3  12 years  gdpusch  Added FIGV support. -- /gdp
make_genome_dir_for_close.pl  1.9  12 years  gdpusch  Fixed handling of spliced loci. -- /gdp
promote_orfs_to_pegs.pl  1.13  12 years  gdpusch  Final clean-up. -- /gdp
find_special_proteins.pl  1.4  11 years  gdpusch  Suppress writing "called_by" and "special_pegs" when "-keep" is selected. -- /gd...
renumber_features.pl  1.11  12 years  gdpusch  Added option to print out ID map. -- /gdp
make_calls_for_start_predictions.pl  1.4  12 years  gdpusch  Added FIGV support. -- /gdp
find_genes_in_families.pl  1.20  12 years  gdpusch  Final clean-up. -- /gdp
genome_peg_dna.pl  1.3  12 years  golsen  Extensive modifications to allow more options, and handle large genomes by not r...
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  1.6  13 years  golsen  Modifications to control ordering of sequences in representative sets and in seq...
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.
load_dlits.pl  1.5  12 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
sync_new_system.pl  1.6  14 years  golsen  Just adding a newline at end of file to make repository match my working copy. ...
compute_translation_MD5.c  1.1  12 years  golsen  Support of MD5 hash codes for SEED translations.
export_dlits.pl  1.2  12 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
load_ec_names.pl  1.5  14 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
fig_net.pl  1.4  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
make_proml_tree.pl  1.6  13 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
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...
index_translation_files.c  1.5  11 years  golsen  Add J as a valid amino acid.
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.
compute_genome_counts.pl  1.16  13 years  golsen  Fix bug introduced in trying to trim "root" from taxonomies.
make_proml_tree_0.pl  1.1  13 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
conditionally_assign.pl  1.4  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
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...
alignment_to_html.pl  1.1  13 years  golsen  A command line script for converting fasta alignments to html. Accesses much of...
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...
fig.pl  1.133  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  12 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
representative_sequences.pl  1.4  13 years  golsen  Modifications to control ordering of sequences in representative sets and in seq...
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_prodom.pl  1.6  13 years  hwang  Change url for prodom's post
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
check_model_v2.pl  1.1  12 years  mkubal  for Model Repository Oct 2007
make_model_spreadsheets.pl  1.1  12 years  mkubal  v1
make_interpro_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
run_flux_optimization.pl  1.3  12 years  mkubal  error checking
make_PDB_attributes.pl  1.2  13 years  mkubal  fix to score format
find_missing_lib_inputs_v2.pl  1.1  12 years  mkubal  for Model Repository Oct 2007
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
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
check_for_scenario_reachability.pl  1.2  12 years  mkubal  identifiesspecific missing input substrate
make_pir_ontology.pl  1.3  12 years  mkubal  provides usage when no argument given
find_model_cofactors.pl  1.6  12 years  mkubal  more error checking
blast_pdb_against_nr_on_tla.pl  1.1  13 years  mkubal  blast pdb against nr
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
make_MFA_tool_input.pl  1.1  12 years  mkubal  fixed formatting errors
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
find_model_information_v2.pl  1.1  12 years  mkubal  for Model Repository Oct 2007
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
make_MPS_model_v2.pl  1.1  12 years  mkubal  for Model Repository Oct 2007
run_remote_Phobius_for_genomes.pl  1.1  12 years  mkubal  run for all complete prok genomes
run_remote_Phobius_for_genome_for_RAST.pl  1.1  12 years  mkubal  for use with RAST server
run_model_generation_v3.pl  1.2  12 years  mkubal  changed ouput to model_files.tgz
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.
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.
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.
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.
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.
load_bbhs.pl  1.15  12 years  olson  *** empty log message ***
filter_pegs_in_subsystems.pl  1.4  14 years  olson  Add license words.
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.
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  1.6  14 years  olson  Add license words.
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.
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.
connections_between.pl  1.6  12 years  olson  add FIGV support, use strict
align_fasta.pl  1.2  14 years  olson  Add license words.
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...
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.
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.
backfill_gaps.pl  1.17  12 years  olson  fix typo
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.
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.
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.
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  1.1  12 years  olson  new scripts
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.
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...
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.
generate_pinned_homologs.pl  1.2  14 years  olson  Add license words.
apply_map.pl  1.2  14 years  olson  Add license words.
make_indexes.pl  1.15  12 years  olson  disable attribute indexing.
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.
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  1.2  14 years  olson  Add license words.
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.
assign_with_no_sims.pl  1.2  14 years  olson  Add license words.
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.
extract_genes.pl  1.5  14 years  olson  Add license words.
blastp_pseq.pl  1.4  14 years  olson  Add license words.
clean_sims.pl  1.2  14 years  olson  Add license words.
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
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_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.
seed2genbank.pl  1.3  13 years  olson  Tweak outptu file handling, expand '%g' into genome name. Allow diret output int...
rapid_propagation.pl  1.69  11 years  olson  Rollup of RAST release changes.
make_sprout_upstream.pl  1.2  14 years  olson  Add license words.
parse_mart.py  1.6  14 years  olson  Add license words.
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.
map_sims_for_bigfc.pl  1.2  14 years  olson  Add license words.
index_sims.pl  1.11  13 years  olson  compute_pchs_from_sims.pl
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.
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_insert.pl  1.2  14 years  olson  Add license words.
where_does_seq_hit.pl  1.2  14 years  olson  Add license words.
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.
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...
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.
potentially_cotranscribed.pl  1.2  14 years  olson  Add license words.
p2p_sync_cron.pl  1.3  14 years  olson  Add license words.
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.
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.
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.
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.
trim_sequences.pl  1.6  14 years  olson  Add license words.
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
pegs_in_subsystem.pl  1.5  14 years  olson  Add license words.
start_services.pl  1.12  14 years  olson  Add license words.
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.
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
compare_figfam_release_results.pl  1.4  12 years  olson  Introduct &FIG::get_figfams_data()
load_literature.pl  1.3  14 years  olson  Add license words.
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.
generate_sprout_links.pl  1.2  14 years  olson  Add license words.
init_FIG.pl  1.9  14 years  olson  SQLite support.
gi2fig.pl  1.3  14 years  olson  Add license words.
load_peg_mapping.pl  1.9  12 years  olson  bah. it's all fine to ask for a table name on the command line, but it helps if ...
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.
restore_assignments.pl  1.2  14 years  olson  Add license words.
load_coupling.pl  1.9  14 years  olson  Remove debugging.
Makefile  1.21  12 years  olson  add md5 modl
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  13 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.
reformat_dsim_dbs.pl  1.2  14 years  olson  Add license words.
p2p_daemon.pl  1.2  14 years  olson  Add license words.
meta.pl  1.9  12 years  olson  Introduct &FIG::get_figfams_data()
generate_intergenic_blocks.pl  1.3  14 years  olson  Add license words.
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
extract_DNA_for_whole_ORFs.pl  1.3  14 years  olson  Add license words.
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.
subtree_of.pl  1.2  14 years  olson  Add license words.
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.
index_contigs.pl  1.11  14 years  olson  Add license words.
all_bbhs.pl  1.16  12 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
genomes_of.pl  1.2  14 years  olson  Add license words.
build_access_sets.pl  1.2  14 years  olson  Add license words.
report_changes.pl  1.2  14 years  olson  Add license words.
expand_blast_table.pl  1.2  14 years  olson  Add license words.
compute_changed_ids_for_nrs.pl  1.4  14 years  olson  Add license words.
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.
index_sims_file.c  1.3  14 years  olson  Doh, put proper comments in for C code.
uninstall.pl  1.2  14 years  olson  Add license words.
register_features_batch.pl  1.2  14 years  olson  Add license words.
make_annotations_for_sprout.pl  1.12  14 years  olson  Add license words.
make_transferable_chunks.pl  1.4  14 years  olson  Add license words.
package_code.pl  1.2  14 years  olson  Add license words.
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.
make_phob_from_seqs.pl  1.7  14 years  olson  Add license words.
get_ss_connections.pl  1.11  13 years  olson  don't crash on missing SS
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.
pegs.pl  1.3  14 years  olson  Add license words.
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  1.4  14 years  olson  Add license words.
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.
fasta_for_hypo.pl  1.2  14 years  olson  Add license words.
pp.pl  1.3  14 years  olson  Add license words.
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.
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  1.11  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
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  1.35  12 years  olson  *** empty log message ***
make_external_sequence_data.pl  1.2  13 years  olson  remove .pl from invocations
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.
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.
test_figfam_placement_into_families.pl  1.9  12 years  olson  Introduct &FIG::get_figfams_data()
import_subsystems.pl  1.22  14 years  olson  Add license words.
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  1.4  12 years  olson  *** empty log message ***
generate_pin_caches.pl  1.5  14 years  olson  Add license words.
list_genomes.pl  1.2  14 years  olson  Add license words.
analyze_scenario_connections.pl  1.3  13 years  olson  add FIGV support.
peg_to_name.pl  1.4  14 years  olson  Add license words.
distribute_attributes.pl  1.11  14 years  olson  Add license words.
rationalize_blast.pl  1.3  14 years  olson  Add license words.
load_chromosomal_clusters.pl  1.2  14 years  olson  Add license words.
ensure_genome_registration.pl  1.1  13 years  olson  generate feature registration stuff
make_reaction_network.pl  1.1  13 years  olson  Hope College modifications.
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
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
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
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
flattened_to_fasta.pl  1.1  14 years  overbeek  add some minor utilities to flatten/unflatten fasta files
load_go.pl  1.2  13 years  overbeek  put in the fr2go stuff
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
cluster_objects.pl  1.3  12 years  overbeek  generalize cluster_objects
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
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
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
check_subsystems.pl  1.7  13 years  overbeek  strip comments on functions for subsystem checking
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...
score_ifcs_mcauliffe.pl  1.2  13 years  overbeek  RAE: correcting indirect functional coupling score
sketch_tree.pl  1.2  13 years  overbeek  add ability to insert sequences into a tree
seed2pir.pl  1.3  14 years  overbeek  RAE: moving PIRSF to links
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
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  1.13  11 years  overbeek  only nonaux roles
install_partition_reps.pl  1.1  12 years  overbeek  add program to install partition representatives in FigfamsData
assess_gene_call_quality.pl  1.10  13 years  overbeek  Added brute-force "-no_fatal" hack to convert FATALs to WARNINGs. -- /gdp
split_and_trim_sequences.pl  1.14  13 years  overbeek  fix problem when repeats occur
find_bad_conflicts.pl  1.1  14 years  overbeek  fixes to wseekly statistics
generate_GO_attributes.pl  1.1  13 years  overbeek  add GO attribute genertation
indirect_functional_coupling_mcauliffe.pl  1.5  13 years  overbeek  indirect functional coupling should not be from a PEG to itself
make_partition_reps_worker.pl  1.1  12 years  overbeek  add program orf computing representative sequences for the partitions
compute_ev_code_attributes.pl  1.2  12 years  overbeek  do not include cluster-based subsystems in forming evidence codes
index_translations.pl  1.20  11 years  overbeek  increase bound on maximum number of sequences
merge_families.pl  1.3  12 years  overbeek  add strip comments argument on function_of
assess_completeness.pl  1.8  14 years  overbeek  leave master: on subsystem_curator
get_translations.pl  1.3  14 years  overbeek  get_translations can take PEG ids from STDIN
potentially_missed_assignments.pl  1.1  13 years  overbeek  add potentially_missed_assignments
make_neigh_joining_tree.pl  1.8  13 years  overbeek  debugged version of bring_tree_up_to_ali
tips_of.pl  1.3  13 years  overbeek  add insert_prot_into_tree, a new way to insert proteins into a tree
make_proposed_assignments_for_consistency.pl  1.4  14 years  overbeek  fixes to wseekly statistics
generate_partitions_worker.pl  1.1  12 years  overbeek  code to generate partitions for FIGfams
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
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
generate_ilits.pl  1.2  12 years  overbeek  code relating to dlit/ilit maintenance
figfam.pl  1.22  12 years  overbeek  add connections between FIGfams and structures
rapid_subsystem_inference.pl  1.13  12 years  overbeek  fixes to inference of -1 variants
update_fr2go.pl  1.1  13 years  overbeek  put in the fr2go stuff
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
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
index_subsystems.pl  1.10  13 years  overbeek  add comments to functions
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
correct_frameshifts.pl  1.13  12 years  overbeek  shift position of correct_frameshifts in rapid_propagation pipeline
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
partition_prots.pl  1.2  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
make_kegg_files.pl  1.5  13 years  overbeek  Update parsing of NAME field to reflect change in source file. -- /gdp
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  1.13  13 years  overbeek  Added 'noEdoBLAST' flag. -- /gdp
make_uniprot_corr.pl  1.2  12 years  overbeek  build uniprot correspondence
generate_partitionsP.pl  1.3  12 years  overbeek  write concatenated output to STDOUT
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
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
package_subsystems.pl  1.5  14 years  overbeek  fixes to deleted_features, replace_features_with, etc
make_partition_repsP.pl  1.1  12 years  overbeek  add program orf computing representative sequences for the partitions
functionally_coupled.pl  1.7  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
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
trimmed_kernel_alignment.pl  1.1  13 years  overbeek  add last round of phylogeny tools
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
pull_fasta_entries.pl  1.7  14 years  overbeek  Fixed switch-parsing bug. -- /gdp
compare_tbls.pl  1.5  13 years  overbeek  Minor change to output. -- /gdp
pull_orfs.pl  1.4  14 years  overbeek  Fixed case-sensitivity bug. -- /gdp
filter_overlaps.pl  1.5  13 years  overbeek  Added some more diagnosting lines. -- /gdp
update_taxonomies.pl  1.8  13 years  overbeek  set longer gap between accessing NCBI
are_close.pl  1.1  14 years  overbeek  fixes to extract_genomes
make_trimmed_alignment_from_ids.pl  1.13  12 years  overbeek  return empty list of failure to open FIFfam
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
check_all_subsystems.pl  1.10  12 years  overbeek  fix bug in check_all_subsystems
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
make_timestamps.pl  1.4  13 years  overbeek  add initial version of FIGO.pm - OO services
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
myjoin.pl  1.1  14 years  overbeek  fix building FigFamData
index_translations_MD5.pl  1.2  11 years  overbeek  increase bound on maximum number of sequences
fc_figfams.pl  1.2  12 years  overbeek  fixes to fc_figfams
split_by_genome.pl  1.1  13 years  overbeek  split_by_genome can be used to split a score or BBH file
find_neighbors.pl  1.30  12 years  overbeek  return empty list of failure to open FIFfam
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  1.5  14 years  overbeek  fixes to usable_subsystem
sims_all.pl  1.5  13 years  overbeek  Added '-no_redo_blast' switch. -- /gdp
ff.pl  1.6  12 years  overbeek  add connections between FIGfams and structures
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
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
aclh.pl  1.11  12 years  paarmann  added new parameter to dump contribs
genbank2fasta.pl  1.1  12 years  paarmann  minimal version to extract fasta from genbank
aclh_reload_contrib.pl  1.1  12 years  paarmann  script to reload the contrib dbs of the aclh
exclude_genomes.pl  1.3  12 years  parrello  Fixed a POD error.
import_similarity_bundle.pl  1.3  12 years  parrello  Fixed a POD error.
make_close.pl  1.7  14 years  parrello  Fixed obsolete form of boundaries_of.
load_attributes.pl  1.45  12 years  parrello  Changed POD format for better compatability with Wiki.
LigandCleanup.pl  1.2  12 years  parrello  Removed obsolete use clases.
NMPDRAnalysis.pl  1.5  12 years  parrello  Removed obsolete use clauses.
PickGeneBoundariesTest.pl  1.1  12 years  parrello  Test script for backfill.
OneShotAttributeAdder.pl  1.2  12 years  parrello  Removed obsolete use clauses.
TransactFeatures.pl  1.20  12 years  parrello  Removed obsolete use clause.
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.
cache_comparison_data.pl  1.9  12 years  parrello  Added a use Carp.
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  14 years  parrello  Fixed obsolete form of boundaries_of.
WikiMaker.pl  1.5  11 years  parrello  Fixed unlinking to be more robust.
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.
trace.pl  1.3  12 years  parrello  Fixed so that the destination is not case-sensitive.
check_model.pl  1.6  12 years  parrello  Fixed a POD error.
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
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
seed2gff.pl  1.36  12 years  redwards  getting rid of need for strain info
gff_statistics.pl  1.1  13 years  redwards  releasing gff statistics
adjacent.pl  1.3  12 years  redwards  changing chop to chomp
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
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  1.21  12 years  redwards  removing error messages
pubmed_gene2peg.pl  1.2  13 years  redwards  making sure gene id is right
correct_gff_missing_contigs.pl  1.5  12 years  redwards  correcting a weird error
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  1.28  13 years  redwards  Just adding comments and docs
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'...
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 ***
parse_genbank.pl  1.17  12 years  wilke  ids have prefixes now , e.g for locus tags locus|ID

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