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Index of /FigKernelScripts

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File Rev. Age Author Last log entry
 Parent Directory        
COPYING.TXT  1.1  13 years  olson  add license file
Consistency_Families.pm  1.1  11 years  bartels  *** empty log message ***
KeyDump.pl  1.1  12 years  parrello  Added to produce the table of attribute keys.
LigandCleanup.pl  1.2  11 years  parrello  Removed obsolete use clases.
Makefile  1.21  11 years  olson  add md5 modl
Makefile.cprogs  1.2  11 years  olson  Support compilation of nap.c
NMPDRAnalysis.pl  1.5  11 years  parrello  Removed obsolete use clauses.
OneShotAttributeAdder.pl  1.2  11 years  parrello  Removed obsolete use clauses.
Packager.pl  1.7  11 years  parrello  Changed POD format for better compatability with Wiki.
PickGeneBoundariesTest.pl  1.1  11 years  parrello  Test script for backfill.
README  1.1.1.1  15 years  efrank   import
Simple.pl  1.4  13 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
SpanishInquisition.pl  1.1  11 years  parrello  Added for testing the Confess method.
TestLocations.pl  1.8  11 years  parrello  Converted to use new name for Contrain method.
TransactFeatures.pl  1.20  11 years  parrello  Removed obsolete use clause.
WikiMaker.pl  1.4  11 years  parrello  Fixed to ignore CVS directories.
aclh.pl  1.11  11 years  paarmann  added new parameter to dump contribs
aclh_reload_contrib.pl  1.1  11 years  paarmann  script to reload the contrib dbs of the aclh
add_assertions_of_function.pl  1.35  11 years  olson  *** empty log message ***
add_assignments.pl  1.3  13 years  olson  Add license words.
add_attributes_from_file.pl  1.1  12 years  redwards  just a simple attribute loader
add_close_genes.pl  1.2  13 years  olson  Add license words.
add_figbar_and_genome_attributes.pl  1.1  12 years  mkubal  v1
add_prots_to_tree.pl  1.1  12 years  golsen  New script for adding proteins to an existing tree.
add_rbs_data_for_start_predictions.pl  1.3  11 years  gdpusch  Added FIGV support. -- /gdp
add_sim_data_for_start_predictions.pl  1.8  11 years  gdpusch  Added FIGV support. -- /gdp
add_start_data_for_start_predictions.pl  1.4  11 years  gdpusch  Added FIGV support. -- /gdp
add_structured_english.pl  1.4  11 years  disz  Added escape arg to structured engkish
add_to_alignment.pl  1.6  12 years  golsen  Modifications to control ordering of sequences in representative sets and in seq...
add_to_subsystems.pl  1.1  13 years  overbeek  add add_to_subsystems
adjacent.pl  1.3  11 years  redwards  changing chop to chomp
ali_to_seq.pl  1.2  13 years  olson  Add license words.
ali_tree.pl  1.4  12 years  overbeek  add strip comments argument on function_of
alias2fig.pl  1.2  13 years  olson  Add license words.
aliases_of.pl  1.6  13 years  olson  Add license words.
align_fasta.pl  1.2  13 years  olson  Add license words.
align_seqs.pl  1.1  12 years  overbeek  add utilities for computing alignments
align_with_clustal.pl  1.8  13 years  olson  Add license words.
align_with_clustal_2.pl  1.4  12 years  golsen  Trivial format change.
alignment_to_html.pl  1.1  12 years  golsen  A command line script for converting fasta alignments to html. Accesses much of...
all_bbhs.pl  1.16  12 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
all_subsystems.pl  1.2  13 years  olson  Add license words.
alter_tbl.pl  1.4  13 years  olson  Add license words.
analyze_scenario_connections.pl  1.3  12 years  olson  add FIGV support.
apply_map.pl  1.2  13 years  olson  Add license words.
apply_peg_changes_to_subsystem.pl  1.3  13 years  olson  Add license words.
are_close.pl  1.1  13 years  overbeek  fixes to extract_genomes
assess_completeness.pl  1.8  13 years  overbeek  leave master: on subsystem_curator
assess_gene_call_quality.pl  1.10  12 years  overbeek  Added brute-force "-no_fatal" hack to convert FATALs to WARNINGs. -- /gdp
assign.pl  1.2  13 years  olson  Add license words.
assign_synonym_ids.pl  1.2  13 years  olson  Add license words.
assign_synonym_ids_to_nr.pl  1.2  13 years  olson  Add license words.
assign_synonym_ids_to_sims.pl  1.2  13 years  olson  Add license words.
assign_to_close_strains.pl  1.10  13 years  overbeek  fixes to Assignments.pm
assign_to_hypo.pl  1.3  13 years  olson  Add license words.
assign_to_sets.pl  1.5  13 years  olson  Add license words.
assign_to_unchanged.pl  1.2  13 years  olson  Add license words.
assign_towards_subsystems.pl  1.2  13 years  olson  Add license words.
assign_using_ff.pl  1.3  11 years  arodri7  update changes
assign_with_no_sims.pl  1.2  13 years  olson  Add license words.
auto_assign.pl  1.19  11 years  olson  Add -orgdir option to use FIGV and its indexed sims.
backfill_gaps.pl  1.17  11 years  olson  fix typo
backup_critical_data.pl  1.4  13 years  olson  Add license words.
backup_subsystems.pl  1.3  11 years  parrello  Fixed a POD error.
bayes_expected_start_scores.pl  1.3  12 years  overbeek  Added comments to expalin logic. -- gdp
bbhs.pl  1.7  13 years  olson  Add license words.
best_hits.pl  1.2  13 years  olson  Add license words.
best_tree_using_proml_on_cluster.pl  1.1  12 years  overbeek  add best_tree_using_proml_on_cluster
bielefeld_tarfile_to_seed.pl  1.7  13 years  overbeek  Tweaked usage msg. -- /gdp
blast2gff.pl  1.21  12 years  redwards  removing error messages
blast_pdb_against_nr_on_tla.pl  1.1  12 years  mkubal  blast pdb against nr
blast_request.pl  1.2  13 years  olson  Add license words.
blastn_chunks.pl  1.3  12 years  overbeek  initial, undebugged version of edit_feature.cgi
blastn_seqs.pl  1.2  13 years  olson  Add license words.
blastp_pseq.pl  1.4  13 years  olson  Add license words.
boot_cluster_seed.pl  1.5  13 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
break_scaffolds.pl  1.2  13 years  olson  Add license words.
bring_system_up_to_date.pl  1.2  13 years  olson  Add license words.
bring_tree_up_to_ali.pl  1.5  12 years  overbeek  debugged version of bring_tree_up_to_ali
build_access_sets.pl  1.2  13 years  olson  Add license words.
build_alignments_for_subsystems.pl  1.4  13 years  olson  Add license words.
build_alignments_from_spreadsheet.pl  1.7  13 years  redwards  using is_environmental
build_anno_clearinghouse.pl  1.6  11 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
build_excel_gene_table.pl  1.3  13 years  olson  Add license words.
build_exemplar_fasta.pl  1.3  13 years  olson  Add license words.
build_figfam_pssm_db.pl  1.2  12 years  gdpusch  Major modifications to &load_family_ids()
build_initial_objects_for_start_predictions.pl  1.12  11 years  gdpusch  Modified to also work on new genomes using "FIGV.". -- /gdp
build_new_figfam_release.pl  1.4  11 years  arodri7  made default procedure the ross hack for new families
build_nohit_fasta.pl  1.2  13 years  olson  Add license words.
build_nr.pl  1.22  11 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
build_nr_sources.pl  1.14  12 years  olson  Rollup of various rast-related changes.
build_partition_index.pl  1.1  11 years  overbeek  return empty list of failure to open FIFfam
build_protein_families.pl  1.5  13 years  olson  Add license words.
build_syn.pl  1.2  13 years  olson  Add license words.
cache_comparison_data.pl  1.9  11 years  parrello  Added a use Carp.
cat_spreadsheet.pl  1.2  13 years  olson  Add license words.
changed_starts.pl  1.7  13 years  olson  Add license words.
check_alignment.pl  1.2  13 years  olson  Add license words.
check_all_lost_sims.pl  1.2  13 years  olson  Add license words.
check_all_subsystems.pl  1.10  11 years  overbeek  fix bug in check_all_subsystems
check_and_extend_all_subsystems.pl  1.7  12 years  overbeek  fix call to rapid_subsystem_extension in check_and_extend_all_subsystems
check_changes_in_organisms.pl  1.2  13 years  olson  Add license words.
check_fast_sims.pl  1.2  13 years  olson  Add license words.
check_fasta_for_dups.pl  1.1  12 years  olson  Missing scripts.
check_figfams.pl  1.6  11 years  olson  Introduct &FIG::get_figfams_data()
check_for_possible_mobile_elements.pl  1.1  12 years  overbeek  add code to search for mobile elements
check_for_scenario_reachability.pl  1.2  11 years  mkubal  identifiesspecific missing input substrate
check_for_unique_sims.pl  1.2  13 years  olson  Add license words.
check_hope_info.pl  1.3  11 years  dejongh  hope script
check_lost_sims.pl  1.2  13 years  olson  Add license words.
check_model.pl  1.6  11 years  parrello  Fixed a POD error.
check_model_v2.pl  1.1  12 years  mkubal  for Model Repository Oct 2007
check_nr_and_peg_synonyms.pl  1.2  13 years  olson  Add license words.
check_peg_assignments.pl  1.3  13 years  olson  Add license words.
check_peg_placement.pl  1.1  11 years  overbeek  redone FIGfam stuff
check_sims_basic.pl  1.8  13 years  redwards  using is_environmental instead of seven 9s
check_sims_syntax.pl  1.3  13 years  olson  Add license words.
check_starts_for_peg_sets.pl  1.5  13 years  olson  Add license words.
check_starts_for_pegs.pl  1.5  13 years  olson  Add license words.
check_subs_and_split_warnings.pl  1.3  11 years  overbeek  minor fix to handle deleted subsystems
check_subsystems.pl  1.7  12 years  overbeek  strip comments on functions for subsystem checking
check_tbl.pl  1.2  13 years  olson  Add license words.
clean_sims.pl  1.2  13 years  olson  Add license words.
clean_subsystems.pl  1.2  13 years  olson  Add license words.
close_connections.pl  1.2  12 years  overbeek  add strip comments argument on function_of
clustal2fasta.pl  1.2  13 years  olson  Add license words.
clustal_to_fasta.pl  1.2  13 years  olson  Add license words.
cluster_by_bbhs.pl  1.2  13 years  olson  Add license words.
cluster_by_sim.pl  1.2  13 years  olson  Add license words.
cluster_objects.pl  1.3  11 years  overbeek  generalize cluster_objects
collect_related_sequences.pl  1.3  12 years  golsen  Encapsulate all of the SEED-dependent functions in the perl module. It should st...
compareMR.pl  1.1  12 years  overbeek  basic stuff for comparing metabolic reconstructions
compare_figfam_release_results.pl  1.4  11 years  olson  Introduct &FIG::get_figfams_data()
compare_scenarios.pl  1.4  11 years  dejongh  Hope College updates
compare_tbls.pl  1.5  12 years  overbeek  Minor change to output. -- /gdp
compare_tree_and_alignment.pl  1.2  13 years  olson  Add license words.
complete_genomes.pl  1.7  13 years  olson  Add license words.
compute_CELLO_and_TMPRED.pl  1.2  12 years  mkubal  test for dir exist
compute_changed_ids_for_nrs.pl  1.4  13 years  olson  Add license words.
compute_contig_md5.pl  1.4  12 years  olson  rollup of metagenome server changes
compute_crc64_for_all_pegs.pl  1.1  12 years  mkubal  v1
compute_dbdir_checksum.pl  1.3  13 years  olson  more checksum fixes. need to replace the "ls -lR" hack with somethign that trave...
compute_ev_code_attributes.pl  1.2  11 years  overbeek  do not include cluster-based subsystems in forming evidence codes
compute_extra_dlit_data.pl  1.4  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
compute_genome_counts.pl  1.16  12 years  golsen  Fix bug introduced in trying to trim "root" from taxonomies.
compute_genome_similarity.pl  1.1  12 years  olson  Missing scripts.
compute_mw_and_pi.pl  1.2  12 years  mkubal  one genome at a time
compute_mw_and_pi_with_BioPerl.pl  1.1  12 years  mkubal  computes mw and pi for all pegs in complete genomes
compute_new_ids.pl  1.2  13 years  olson  Add license words.
compute_pchs_from_sims.pl  1.2  12 years  olson  Rollup of changes for the new RAST install.
compute_pins.pl  1.4  11 years  olson  undo bogus commit
compute_pins_and_clusters.pl  1.2  13 years  olson  Add license words.
compute_potential_fusions.pl  1.12  13 years  overbeek  fix to fusions
compute_sim_chunk.pl  1.3  13 years  olson  add working-on-chunk support
compute_simple_scores.pl  1.4  13 years  olson  Add license words.
compute_translation_MD5.c  1.1  11 years  golsen  Support of MD5 hash codes for SEED translations.
condense_blast.pl  1.2  13 years  olson  Add license words.
conditionally_assign.pl  1.3  13 years  olson  Add license words.
connect_PDB_to_FIGfams.pl  1.1  11 years  arodri7  update changes
connect_PDB_to_FIGfams_worker.pl  1.1  11 years  arodri7  update changes
connections_between.pl  1.6  12 years  olson  add FIGV support, use strict
correct_frameshifts.pl  1.13  11 years  overbeek  shift position of correct_frameshifts in rapid_propagation pipeline
correct_gff_missing_contigs.pl  1.5  11 years  redwards  correcting a weird error
count_bases.pl  1.2  13 years  olson  Add license words.
crc64.py  1.1  11 years  mkubal  uses for mapping of interpro downlaod to pegs
createTIGRfamSrc.pl  1.1  11 years  bartels  *** empty log message ***
create_sims_btree.pl  1.1  13 years  olson  BTREE-index versions of these. Experimental still.
curator_of.pl  1.1  13 years  overbeek  minor fixes to assignment for close strains
das_test.pl  1.2  13 years  olson  Add license words.
db_xrefs_of.pl  1.4  13 years  olson  Add license words.
delete_all_attribute_files.pl  1.2  13 years  overbeek  RAE: New delete attribute files to remove all files. maybe this will work
delete_genomes_from_sims.pl  1.2  13 years  olson  Add license words.
diff_tbls.pl  1.1  13 years  overbeek  Computes difference betwween two tbl files. -- /gdp
direct_functional_coupling.pl  1.4  12 years  overbeek  tighten length constraints for figfam matching
display_tree.pl  1.4  13 years  olson  Add license words.
distribute_attributes.pl  1.11  13 years  olson  Add license words.
dna_seq.pl  1.2  13 years  olson  Add license words.
dump_attributes.pl  1.2  13 years  olson  Add license words.
dump_machine_state.pl  1.3  13 years  olson  Add license words.
embl2gff.pl  1.20  13 years  olson  Add license words.
embl2gff_addmd5.py  1.2  13 years  olson  Add license words.
ensure_genome_registration.pl  1.1  12 years  olson  generate feature registration stuff
ev_code_cron.pl  1.15  11 years  parrello  Modified to use the new evidence code loader.
evaluate_quality_of_trees.pl  1.4  12 years  overbeek  debugged version of bring_tree_up_to_ali
exclude_genomes.pl  1.3  11 years  parrello  Fixed a POD error.
expand_blast_table.pl  1.2  13 years  olson  Add license words.
expand_multifunctional_roles.pl  1.3  13 years  olson  Add license words.
expand_sims.pl  1.2  11 years  olson  *** empty log message ***
expand_transferred_chunks.pl  1.4  13 years  olson  Add license words.
explore_subsys_pmid.pl  1.5  12 years  hwang  PEG information is no longer stored in the file. Parsing of the file in this scr...
export_ACH_resolution_DB.pl  1.2  11 years  overbeek  fixes relating to comments
export_dlits.pl  1.2  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
export_genome_as_gff.pl  1.6  13 years  olson  Add license words.
export_similarity_request.pl  1.3  13 years  overbeek  minor fixes to assignment for close strains
export_subsystem_as_gff.pl  1.2  13 years  olson  Add license words.
extend_subsys.pl  1.7  13 years  redwards  using is_environmental instead of seven 9s
extend_subsystem.pl  1.2  13 years  olson  Add license words.
external_calls.pl  1.2  13 years  olson  Add license words.
extract_DNA_for_whole_ORFs.pl  1.3  13 years  olson  Add license words.
extract_DNA_sequence_from_object_for_start_predictions.pl  1.2  13 years  olson  Add license words.
extract_data_for_syncing_after_update.pl  1.6  13 years  olson  Add license words.
extract_data_to_keep.pl  1.5  13 years  olson  Add license words.
extract_fasta_idmap.pl  1.1  13 years  overbeek  RAE: Adding FigKernelScripts/extract_fasta_idmap.pl
extract_genes.pl  1.5  13 years  olson  Add license words.
extract_genomes.pl  1.38  13 years  overbeek  changes to support dynamic sims and updates
extract_sp_links.pl  1.3  12 years  olson  fix -h error
extract_subset_from_sprout_data.pl  1.2  13 years  olson  Add license words.
fast_blastp.pl  1.1  11 years  overbeek  fast_blastp is a tool to support rapid similarity estimates using FIGfam partiti...
fasta_cksum.c  1.4  13 years  olson  Doh, put proper comments in for C code.
fasta_for_hypo.pl  1.2  13 years  olson  Add license words.
fasta_to_phylip.pl  1.2  13 years  olson  Add license words.
fastasize.c  1.3  13 years  olson  Doh, put proper comments in for C code.
fc_figfams.pl  1.2  12 years  overbeek  fixes to fc_figfams
feature_length_histogram.pl  1.3  11 years  gdpusch  Fixed duplicated ID bug, plus minor cosmetic changes. -- /gdp
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...
ff.pl  1.6  11 years  overbeek  add connections between FIGfams and structures
fid2dna.pl  1.2  13 years  olson  Add license words.
fig.pl  1.132  11 years  overbeek  code relating to dlit/ilit maintenance
fig_net.pl  1.3  13 years  olson  Add license words.
fig_rpc.pl  1.3  13 years  olson  Add license words.
fig_specific_sequences.pl  1.3  13 years  redwards  using is_environmental instead of seven 9s
fig_xmlrpc_server.pl  1.5  13 years  olson  Add license words.
figfam.pl  1.22  11 years  overbeek  add connections between FIGfams and structures
figfam_quality_control.pl  1.7  11 years  arodri7  update changes
figfam_size_distribution.pl  1.1  11 years  arodri7  update changes
figfam_subsystems.pl  1.1  11 years  arodri7  update changes
fill_in_cell.pl  1.2  13 years  olson  Add license words.
fill_in_roles.pl  1.4  13 years  olson  Add license words.
fill_subsys.pl  1.5  13 years  olson  Add license words.
filter_figfams.pl  1.2  12 years  overbeek  add computation of alignments to building FIGFAMS
filter_new_overlaps.pl  1.2  13 years  olson  Add license words.
filter_overlaps.pl  1.5  12 years  overbeek  Added some more diagnosting lines. -- /gdp
filter_pegs_in_subsystems.pl  1.4  13 years  olson  Add license words.
filter_tbl_overlaps.pl  1.10  13 years  overbeek  set up find_neighbors to handle existing genomes
find_bad_conflicts.pl  1.1  13 years  overbeek  fixes to wseekly statistics
find_essential_reactions.pl  1.2  12 years  formsma  Fixed incorrect filehandle. Tested Good - Kevin
find_gaps.pl  1.8  11 years  gdpusch  Fixed error in lower boundary constraint. -- /gdp
find_genes_based_on_neighbors.pl  1.22  11 years  gdpusch  Final clean-up. -- /gdp
find_genes_in_families.pl  1.20  11 years  gdpusch  Final clean-up. -- /gdp
find_maximal_clusters.pl  1.2  13 years  olson  Add license words.
find_missing_lib_inputs.pl  1.5  12 years  formsma  Updated error statements. Added compound name printing. - Kevin
find_missing_lib_inputs_v2.pl  1.1  12 years  mkubal  for Model Repository Oct 2007
find_model_cofactors.pl  1.6  12 years  mkubal  more error checking
find_model_information.pl  1.6  12 years  formsma  Changed logic on input prediction for dealing with biomass compounds - Kevin
find_model_information_v2.pl  1.1  12 years  mkubal  for Model Repository Oct 2007
find_neighbors.pl  1.30  11 years  overbeek  return empty list of failure to open FIFfam
find_neighbors_by_sim.pl  1.4  11 years  olson  Add -no-duplicates support for build_anno_clearinghouse and build_nr.
find_neighbors_using_figfams.pl  1.8  11 years  gdpusch  Added comments, divide-by-zero protection, and removed an ill-thought-out hand-o...
find_poss_fs.pl  1.1  11 years  overbeek  add code to fix frameshifts in a genome
find_protein_homologs.pl  1.1  11 years  golsen  Debugging and adding support of all the NCBI genetic codes.
find_selenoproteins.pl  1.4  11 years  golsen  Add functions to reference selenoproteins, and add change the set slightly. Rep...
find_special_proteins.pl  1.3  11 years  gdpusch  Final clean-up. -- /gdp
find_subsys.pl  1.3  11 years  overbeek  allow loose matching in rapid_propagation
fix_annotations.pl  1.2  13 years  olson  Add license words.
fix_eol.pl  1.2  13 years  olson  Add license words.
fix_ext_funcs.pl  1.2  13 years  olson  Add license words.
fix_invalid_fasta.pl  1.1  12 years  redwards  Initial release of programs to check and fix valid fasta format
flatten_fasta.pl  1.1  13 years  overbeek  add some minor utilities to flatten/unflatten fasta files
flattened_to_fasta.pl  1.1  13 years  overbeek  add some minor utilities to flatten/unflatten fasta files
flip_sims.pl  1.7  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
format_peg_dbs.pl  1.3  13 years  olson  Add license words.
function_of.pl  1.4  13 years  olson  Add license words.
functionally_coupled.pl  1.6  12 years  overbeek  corrected functionall_coupled
fusion_of.pl  1.2  13 years  olson  Add license words.
gather_attributes.pl  1.8  13 years  olson  Add license words.
genbank2fasta.pl  1.1  11 years  paarmann  minimal version to extract fasta from genbank
genbank2gff3.pl  1.5  13 years  olson  Add license words.
generate_GO_attributes.pl  1.1  12 years  overbeek  add GO attribute genertation
generate_GenomeGroups_for_sprout.pl  1.3  13 years  olson  Add license words.
generate_Property_for_sprout.pl  1.6  13 years  olson  Add license words.
generate_Source_for_sprout.pl  1.2  13 years  olson  Add license words.
generate_dlit_ev_codes.pl  1.5  11 years  overbeek  switching to new ilidt/dlit stuff
generate_gene_blocks.pl  1.3  13 years  olson  Add license words.
generate_genome_feature_tables_for_sprout.pl  1.16  13 years  olson  Add license words.
generate_ilit_ev_codes.pl  1.4  11 years  overbeek  code relating to dlit/ilit maintenance
generate_ilits.pl  1.2  11 years  overbeek  code relating to dlit/ilit maintenance
generate_input_for_auto_assignments.pl  1.2  13 years  olson  Add license words.
generate_intergenic_blocks.pl  1.3  13 years  olson  Add license words.
generate_kernel_css.pl  1.5  13 years  olson  Add license words.
generate_max_clusters.pl  1.2  13 years  olson  Add license words.
generate_partitionsP.pl  1.3  11 years  overbeek  write concatenated output to STDOUT
generate_partitions_worker.pl  1.1  11 years  overbeek  code to generate partitions for FIGfams
generate_pin_caches.pl  1.5  13 years  olson  Add license words.
generate_pinned_homologs.pl  1.2  13 years  olson  Add license words.
generate_similarities.pl  1.2  13 years  olson  Add license words.
generate_sprout_links.pl  1.2  13 years  olson  Add license words.
generate_subsys_tables_for_sprout.pl  1.8  13 years  olson  Add license words.
genome_peg_dna.pl  1.3  11 years  golsen  Extensive modifications to allow more options, and handle large genomes by not r...
genomes_of.pl  1.2  13 years  olson  Add license words.
genomes_with_essentiality_data.pl  1.1  13 years  redwards  Adding tools to handle essentiality data for Sveta
get_NCBI_genome_attributes.pl  1.1  11 years  arodri7  get_NCBI_genome_attributes searches the NCBI internet sites for genome attribute...
get_best_set_of_genes_for_column.pl  1.3  13 years  olson  Add license words.
get_class_examples.pl  1.2  13 years  olson  Add license words.
get_dna.pl  1.6  11 years  gdpusch  Minor cosmetic change. -- /gdp
get_empty_ecs  1.3  13 years  olson  Add license words.
get_empty_ecs.pl  1.4  13 years  olson  Add license words.
get_ev_codes.pl  1.14  11 years  olson  Introduct &FIG::get_figfams_data()
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
get_fasta_for_tbl_entries.pl  1.9  11 years  gdpusch  Added support for multi-exon locations. -- /gdp
get_figfam_funcs.pl  1.1  13 years  overbeek  add install_anticipated_functions and some FIGfam tracking stuff
get_journals_for_frole.pl  1.1  12 years  hwang  Files to get journal information from PubMed
get_journals_for_org.pl  1.1  12 years  hwang  this script is the backend to get journals using taxonomy id or name. This calls...
get_long_enough.pl  1.2  13 years  olson  Add license words.
get_nr_entries_without_sims.pl  1.4  13 years  olson  Add license words.
get_pathways_for_EC.pl  1.2  13 years  olson  Add license words.
get_potential_starts_for_start_predictions.pl  1.3  11 years  gdpusch  Added FIGV support. -- /gdp
get_pubmed_journals.pl  1.5  12 years  hwang  update comment that this is for peg curation
get_sims_for_start_predictions.pl  1.5  11 years  gdpusch  Added FIGV support. -- /gdp
get_ss_connections.pl  1.11  12 years  olson  don't crash on missing SS
get_subsystem_properties.pl  1.1  12 years  overbeek  minor modifications to get subsystems statistics
get_synonyms_from_ach_for_id.pl  1.2  11 years  wilke  *** empty log message ***
get_taxid_journals.pl  1.1  12 years  hwang  get journals from PMC using taxide
get_translations.pl  1.3  13 years  overbeek  get_translations can take PEG ids from STDIN
gff2Ontology.pl  1.4  13 years  olson  Add license words.
gff2ncbitab.pl  1.3  11 years  olson  add swissprot
gff2seed.pl  1.28  12 years  redwards  Just adding comments and docs
gff2tab.pl  1.5  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
gff_statistics.pl  1.1  12 years  redwards  releasing gff statistics
gi2fig.pl  1.3  13 years  olson  Add license words.
html_parser.py  1.2  13 years  olson  Add license words.
iedb.pl  1.10  13 years  overbeek  RAE: bugger, correcting the array dereferencing
import_external_sequences_step1.pl  1.8  13 years  olson  Add license words.
import_external_sequences_step3.pl  1.5  13 years  olson  Add license words.
import_similarity_bundle.pl  1.3  11 years  parrello  Fixed a POD error.
import_subsystems.pl  1.22  13 years  olson  Add license words.
index-pegsyn.pl  1.1  12 years  olson  Missing scripts.
index-pegsyn2.pl  1.1  11 years  olson  new version of pegsyn indexer that presorts data before inserting into the btree...
index_anno_clearinghouse.pl  1.3  11 years  olson  multiple id support, build fixes
index_annotations.pl  1.11  12 years  olson  bugfix
index_contig_files.c  1.5  13 years  olson  fix to work on 64-bit linux
index_contigs.pl  1.11  13 years  olson  Add license words.
index_fasta.pl  1.2  13 years  olson  Add license words.
index_feature_dir_fasta.pl  1.1  11 years  olson  Index scripts for FIGV accleration.
index_figv_annos.pl  1.1  11 years  olson  Index scripts for FIGV accleration.
index_neighborhoods.pl  1.3  13 years  olson  Add license words.
index_nr.pl  1.2  12 years  olson  compute length btree also
index_pins.pl  1.3  13 years  olson  new pin indexer
index_sims.pl  1.11  12 years  olson  compute_pchs_from_sims.pl
index_sims_file.c  1.3  13 years  olson  Doh, put proper comments in for C code.
index_sprout.pl  1.12  13 years  olson  Add license words.
index_subsystems.pl  1.10  12 years  overbeek  add comments to functions
index_translation_files.c  1.4  13 years  golsen  Commit index_translation_files version 2.01 (use index_translation_files -v) Min...
index_translations.pl  1.19  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
index_translations_MD5.pl  1.1  11 years  golsen  Support of MD5 hash codes for SEED translations.
indirect_functional_coupling.pl  1.5  12 years  overbeek  indirect functional coupling should not be from a PEG to itself
indirect_functional_coupling_mcauliffe.pl  1.5  12 years  overbeek  indirect functional coupling should not be from a PEG to itself
init_FIG.pl  1.9  13 years  olson  SQLite support.
init_dbserver.pl  1.3  13 years  olson  Add license words.
init_maps.pl  1.3  13 years  olson  Add license words.
init_peg_job_scheduler.pl  1.4  13 years  olson  Add license words.
initial_set.pl  1.2  13 years  olson  Add license words.
initialize_alignments_for_subsystems.pl  1.2  13 years  overbeek  fixes to extract_genomes, salvage_subsystem_rows and initialize_alignments_for_s...
initialize_ann_and_ev.pl  1.3  11 years  olson  undo bogus commit
initialize_figfams.pl  1.7  11 years  arodri7  update changes
insert.pl  1.2  13 years  olson  Add license words.
insert_all.pl  1.2  13 years  olson  Add license words.
insert_into_a_tree.pl  1.5  12 years  overbeek  add tree_neighbors and latest phylogeny stuff
insert_prot_into_tree.pl  1.14  12 years  golsen  Continuing the update of tree packages and programs
install-data.pl  1.8  11 years  olson  fix to dvd data installer
install_annotations.pl  1.4  13 years  olson  Add license words.
install_anticipated_functions.pl  1.3  11 years  olson  Introduct &FIG::get_figfams_data()
install_assignments.pl  1.7  13 years  olson  Add license words.
install_code.pl  1.2  13 years  olson  Add license words.
install_feature_updates.pl  1.2  13 years  olson  Add license words.
install_features_batch.pl  1.1  11 years  olson  Add new script to install a batch of genomid.tbl / genomeid.fasta files. Initial...
install_lightweight_code.pl  1.2  13 years  olson  Add license words.
install_new_coupling_data.pl  1.3  12 years  olson  add option to install from a jobdir
install_partition_reps.pl  1.1  11 years  overbeek  add program to install partition representatives in FigfamsData
install_partitions.pl  1.3  11 years  arodri7  update changes
install_rast_batch.pl  1.4  11 years  olson  more fixes
install_subsystems.pl  1.2  13 years  olson  Add license words.
install_translation_rules.pl  1.3  13 years  olson  Add license words.
interval.pl  1.2  13 years  olson  Add license words.
is_archaeal.pl  1.2  13 years  olson  Add license words.
is_bacterial.pl  1.2  13 years  olson  Add license words.
is_eukaryotic.pl  1.2  13 years  olson  Add license words.
is_prokaryotic.pl  1.2  13 years  olson  Add license words.
keep_only.pl  1.2  13 years  olson  Add license words.
lengths_of_contigs.pl  1.2  13 years  olson  Add license words.
list_genomes.pl  1.2  13 years  olson  Add license words.
load_ACH_resolution_DB.pl  1.4  11 years  overbeek  fixes to quotemeta characters in loading comments
load_abstract_coupling.pl  1.3  13 years  parrello  Changed to use a single-character delimiter (for compatability with PostGRES).
load_attributes.pl  1.45  11 years  parrello  Changed POD format for better compatability with Wiki.
load_bbhs.pl  1.15  11 years  olson  *** empty log message ***
load_bbhs_btree.pl  1.1  13 years  olson  BTREE-index versions of these. Experimental still.
load_chromosomal_clusters.pl  1.2  13 years  olson  Add license words.
load_close.pl  1.9  12 years  overbeek  tighten length constraints for figfam matching
load_coupling.pl  1.9  13 years  olson  Remove debugging.
load_coupling_btree.pl  1.1  13 years  olson  BTREE-index versions of these. Experimental still.
load_distances.pl  1.5  13 years  olson  Add license words.
load_dlits.pl  1.5  11 years  golsen  Many code clean-ups in the dlits routines, and associated literature. Add suppo...
load_ec_names.pl  1.5  13 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
load_external_orgs.pl  1.3  13 years  olson  Add license words.
load_features.pl  1.24  11 years  olson  fix tmp file name.
load_go.pl  1.2  12 years  overbeek  put in the fr2go stuff
load_hugo.pl  1.6  13 years  olson  Add license words.
load_id_correspondence.pl  1.3  11 years  olson  updates to the load_id_correspondence loader and searching code.
load_kegg.pl  1.9  12 years  dejongh  *** empty log message ***
load_links.pl  1.6  13 years  olson  Add license words.
load_literature.pl  1.3  13 years  olson  Add license words.
load_local_maps.pl  1.3  13 years  olson  Add license words.
load_locks.pl  1.1  13 years  overbeek  introduce locks on features to block assignments
load_pch_pins.pl  1.2  13 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 ...
load_pirsf.pl  1.14  13 years  overbeek  RAE: correcting load_pirsf not recognizing a firewall
load_protein_families.pl  1.9  13 years  overbeek  RAE: extending protein families
load_sets.pl  1.5  13 years  olson  Add license words.
load_sims.pl  1.10  13 years  olson  If we are loading unmapped files (as generated by make_close -no-map and make_s...
location_of.pl  1.2  13 years  olson  Add license words.
maint-remove-obsolete-aliases.pl  1.1  12 years  olson  Missing scripts.
make_CDD_attributes.pl  1.2  12 years  mkubal  fix to score format
make_CELLO_and_TMPRED_attributes.pl  1.2  12 years  mkubal  changed ; to :: for key separator
make_FigFamsData.pl  1.4  13 years  overbeek  order generated FIGfams
make_IPR_PFAM_GO_attributes.pl  1.3  12 years  mkubal  fix to score format
make_MFA_tool_input.pl  1.1  11 years  mkubal  fixed formatting errors
make_MPS_model.pl  1.6  12 years  formsma  Updated some logic for the sink reactions. Fixes flux issues - Kevin
make_MPS_model_v2.pl  1.1  12 years  mkubal  for Model Repository Oct 2007
make_Ontology_database.pl  1.3  11 years  mkubal  provides usage when no argument given
make_PDB_attributes.pl  1.2  12 years  mkubal  fix to score format
make_PFAM_HMM_derived_attributes.pl  1.2  12 years  mkubal  added date as 2nd argument
make_PHOBs_for_subsystems.pl  1.5  13 years  olson  Add license words.
make_PROSITE_PIR_PRODOM_attributes.pl  1.3  12 years  mkubal  fix to score format
make_Phobius_attributes.pl  1.2  12 years  mkubal  added date as 2nd argument
make_SBML_model.pl  1.5  12 years  formsma  Added reaction ATPSYN for manual since KEGG doesn't have it - Kevin
make_SignalP_attributes.pl  1.2  12 years  mkubal  changed ; to :: for key separator
make_annotations_for_sprout.pl  1.12  13 years  olson  Add license words.
make_assignments_fit_initial_css.pl  1.4  13 years  olson  Add license words.
make_assignments_set.pl  1.3  13 years  olson  Add license words.
make_attribute_index.pl  1.6  13 years  olson  Add license words.
make_binary.pl  1.2  13 years  olson  Add license words.
make_calls.pl  1.4  13 years  olson  Add license words.
make_calls_for_start_predictions.pl  1.4  11 years  gdpusch  Added FIGV support. -- /gdp
make_cdd_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_close.pl  1.7  13 years  parrello  Fixed obsolete form of boundaries_of.
make_close_strain_data.pl  1.13  12 years  overbeek  Added 'noEdoBLAST' flag. -- /gdp
make_close_strain_family_tabs.pl  1.2  13 years  overbeek  fixes to wseekly statistics
make_external_sequence_data.pl  1.2  12 years  olson  remove .pl from invocations
make_fam_tabs.pl  1.5  13 years  overbeek  RAE: Protein Families interface and construction
make_fasta_btree.pl  1.1  12 years  olson  Utility for creating btree access for fasta files.
make_fig_files.pl  1.3  13 years  olson  Add license words.
make_figfam_tree.pl  1.1  11 years  arodri7  update changes
make_figfam_tree_worker.pl  1.1  11 years  arodri7  update changes
make_figfams.pl  1.3  13 years  overbeek  families.2c should get current function - not family function
make_genome_dir_for_close.pl  1.9  11 years  gdpusch  Fixed handling of spliced loci. -- /gdp
make_go_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_indexes.pl  1.15  12 years  olson  disable attribute indexing.
make_interpro_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_jpg.pl  1.2  13 years  olson  Add license words.
make_kegg_files.pl  1.5  12 years  overbeek  Update parsing of NAME field to reflect change in source file. -- /gdp
make_maps_from_sub.py  1.5  13 years  olson  Add license words.
make_match_table.pl  1.2  13 years  olson  Add license words.
make_model_spreadsheets.pl  1.1  12 years  mkubal  v1
make_ncbi_files.pl  1.4  12 years  wilke  changed check for existing directories
make_neigh_joining_tree.pl  1.8  12 years  overbeek  debugged version of bring_tree_up_to_ali
make_occ_counts.pl  1.2  13 years  olson  Add license words.
make_overlap_report.pl  1.20  11 years  gdpusch  No longer complains about split loci. -- /gdp
make_parallel_proml_run.pl  1.2  12 years  overbeek  add rates to phylogeny stuff
make_partition_repsP.pl  1.1  11 years  overbeek  add program orf computing representative sequences for the partitions
make_partition_reps_worker.pl  1.1  11 years  overbeek  add program orf computing representative sequences for the partitions
make_pdb_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_peg_map_from_tbl.pl  1.2  11 years  gdpusch  Removed hard-coded regexps that failed to handle multi-exon loci. -- /gdp
make_peg_maps.pl  1.3  13 years  overbeek  minor fixes
make_peg_maps_from_fasta.pl  1.1  12 years  olson  new scripts
make_pfam_ontology.pl  1.4  11 years  mkubal  provides usage when no argument given
make_phob_from_ids.pl  1.3  13 years  olson  Add license words.
make_phob_from_seqs.pl  1.7  13 years  olson  Add license words.
make_pir_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_proml_tree.pl  1.6  12 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
make_proml_tree_0.pl  1.1  12 years  golsen  Replace make_proml_tree with entirely new version. Move the former version to m...
make_proposed_assignments_for_consistency.pl  1.4  13 years  overbeek  fixes to wseekly statistics
make_prosite_ontology.pl  1.3  11 years  mkubal  provides usage when no argument given
make_protein_sets.pl  1.4  13 years  olson  Add license words.
make_protein_weights_and_rates.pl  1.2  12 years  golsen  Moving some tree building tools into packages.
make_rates.pl  1.2  13 years  olson  Add license words.
make_reaction_network.pl  1.1  12 years  olson  Hope College modifications.
make_reduce_sims_index.pl  1.1  12 years  olson  new script
make_sim_sets.pl  1.3  13 years  olson  Add license words.
make_sim_tab.pl  1.8  12 years  olson  compute_pchs_from_sims.pl
make_sp_desc_with_org.pl  1.2  13 years  olson  Add license words.
make_sp_func_syn_dicts.pl  1.2  13 years  olson  Add license words.
make_sp_org_domain_table.pl  1.2  13 years  olson  Add license words.
make_sp_org_table.pl  1.2  13 years  olson  Add license words.
make_sp_uni_files.pl  1.4  12 years  wilke  changed check for input and output directory the directories may exists, so don'...
make_spreadsheet_and_notes.pl  1.3  13 years  olson  Add license words.
make_sprout_bbhs.pl  1.2  13 years  olson  Add license words.
make_sprout_upstream.pl  1.2  13 years  olson  Add license words.
make_subsys_based_families.pl  1.12  11 years  overbeek  additions to FIGfam maintenance
make_subsystems_from_clusters.pl  1.5  13 years  olson  Add license words.
make_tf_equivalog_file.pl  1.1  11 years  bartels  *** empty log message ***
make_timestamps.pl  1.4  12 years  overbeek  add initial version of FIGO.pm - OO services
make_transferable_chunks.pl  1.4  13 years  olson  Add license words.
make_transferable_tarfiles.pl  1.3  13 years  olson  Add license words.
make_trimmed_alignment_from_ids.pl  1.13  11 years  overbeek  return empty list of failure to open FIFfam
make_uniprot_corr.pl  1.2  11 years  overbeek  build uniprot correspondence
map-nr-ids-to-ncbi-std.pl  1.1  11 years  olson  Script to map IDs in a SEED NR into forms acceptable to the indexed NCBI fasta p...
map_pegs.pl  1.3  13 years  parrello  Fixed obsolete form of boundaries_of.
map_sims.pl  1.5  13 years  olson  Add license words.
map_sims_for_bigfc.pl  1.2  13 years  olson  Add license words.
map_to_scaffold.pl  1.4  11 years  olson  Actually write out the changed entries.
mark_nr.pl  1.2  13 years  olson  Add license words.
match_dna_to_aligned_prots.pl  1.4  13 years  olson  Add license words.
md5.c  1.3  13 years  olson  Doh, put proper comments in for C code.
merge_annotations.pl  1.3  13 years  olson  Add license words.
merge_families.pl  1.3  12 years  overbeek  add strip comments argument on function_of
merge_translation_rules.pl  1.7  13 years  olson  Add license words.
meta.pl  1.9  11 years  olson  Introduct &FIG::get_figfams_data()
metagenome2genbank.pl  1.4  11 years  mkubal  includes data from meta.xml
mg_user_id_to_unique.pl  1.2  11 years  mkubal  full loop
myjoin.pl  1.1  13 years  overbeek  fix building FigFamData
new_versions_of_features.pl  1.1  13 years  overbeek  add new_versions_of_features
nmpdr2gff.pl  1.1  13 years  overbeek  RAE: Changes to gff3 files for NMPDR and adding nmpdr2gff for creating the files...
order_corrections_for_start_predictions.pl  1.5  11 years  gdpusch  Added FIGV support. -- /gdp
order_figfams.pl  1.1  13 years  overbeek  order_figfams
order_seqs_on_length.pl  1.1  12 years  overbeek  add utilities for computing alignments
order_sets.pl  1.3  13 years  olson  Add license words.
p2p_daemon.pl  1.2  13 years  olson  Add license words.
p2p_sync_cron.pl  1.3  13 years  olson  Add license words.
p2p_sync_from_remote.pl  1.4  13 years  olson  Add license words.
package_annotations.pl  1.9  13 years  olson  Add license words.
package_assignments.pl  1.8  13 years  olson  Add license words.
package_code.pl  1.2  13 years  olson  Add license words.
package_lightweight_code.pl  1.2  13 years  olson  Add license words.
package_raw_data_for_transplant.pl  1.2  13 years  olson  Add license words.
package_sims.pl  1.2  13 years  olson  Add license words.
package_subsystems.pl  1.5  13 years  overbeek  fixes to deleted_features, replace_features_with, etc
package_translation_rules.pl  1.2  13 years  olson  Add license words.
paint_tree.pl  1.3  13 years  olson  Add license words.
parse_genbank.pl  1.17  11 years  wilke  ids have prefixes now , e.g for locus tags locus|ID
parse_mart.py  1.6  13 years  olson  Add license words.
parse_uniparc.pl  1.1  12 years  mkubal  v1
partition_prots.pl  1.1  11 years  overbeek  add code to partition proteins to support rapid similarity computations
peg2pubmed.pl  1.1  13 years  hwang  Added two scripts that will generate pubmed files
peg_to_name.pl  1.4  13 years  olson  Add license words.
peg_to_pdb.py  1.2  13 years  olson  Add license words.
peg_to_subsystems.pl  1.3  13 years  olson  Add license words.
pegs.pl  1.3  13 years  olson  Add license words.
pegs_in_conflict.pl  1.3  13 years  olson  Add license words.
pegs_in_subsystem.pl  1.5  13 years  olson  Add license words.
pegs_in_subsystems.pl  1.5  13 years  overbeek  fixes to usable_subsystem
possible_frameshifts.pl  1.1  12 years  overbeek  update possible_frameshifts
possibly_truncated.pl  1.2  13 years  olson  Add license words.
postprocess_computed_sims.pl  1.2  13 years  olson  Add license words.
potentially_cotranscribed.pl  1.2  13 years  olson  Add license words.
potentially_missed_assignments.pl  1.1  13 years  overbeek  add potentially_missed_assignments
pp.pl  1.3  13 years  olson  Add license words.
predict_scenarios.pl  1.2  12 years  formsma  Added code to automatically run 'run_scenarios All' if it hasn't been run. These...
predict_starts.pl  1.8  11 years  gdpusch  Added FIGV support. -- /gdp
prep_viz.pl  1.2  13 years  olson  Add license words.
prepare_metagenome_files_for_download.pl  1.4  11 years  mkubal  full loop
prepare_metagenome_files_for_ftp.pl  1.3  11 years  mkubal  checks for PUBLIC file
process_new_sims.pl  1.6  12 years  olson  Rollup of various rast-related changes.
process_sim_deletions_and_replacements.pl  1.3  13 years  olson  Add license words.
project.pl  1.2  13 years  olson  Add license words.
promote_orfs_to_pegs.pl  1.13  11 years  gdpusch  Final clean-up. -- /gdp
propagate_subsys_changes_to_figfams.pl  1.9  11 years  arodri7  update changes
pubmed_gene2peg.pl  1.2  13 years  redwards  making sure gene id is right
pull_fasta_entries.pl  1.7  13 years  overbeek  Fixed switch-parsing bug. -- /gdp
pull_orfs.pl  1.4  13 years  overbeek  Fixed case-sensitivity bug. -- /gdp
pull_sp_entries.pl  1.2  13 years  olson  Add license words.
purge_fasta.pl  1.1  13 years  overbeek  Removes duplicate entries from fasta file. -- /gdp
purge_tbl.pl  1.1  13 years  overbeek  Removes duplicate entries from tbl file. -- /gdp
put_directory_in_one_file.pl  1.2  13 years  olson  Add license words.
questionable_calls.pl  1.2  13 years  olson  Add license words.
rapid_propagation.pl  1.68  11 years  olson  fix another gc=4 bug
rapid_subsystem_inference.pl  1.13  11 years  overbeek  fixes to inference of -1 variants
rationalize_blast.pl  1.3  13 years  olson  Add license words.
read_write_excel.pl  1.1  13 years  overbeek  RAE: Initial release of a simple script to read and write excel files to allow e...
rebuild_global_chromosomal_clusters.pl  1.2  12 years  overbeek  version of rebuild_global_chromosomal_clusters that works
recompute_comparison.pl  1.1  11 years  bartels  *** empty log message ***
reduce_sims.pl  1.11  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
reformat_contigs.pl  1.14  11 years  olson  add max id fix, infinte loop fix.
reformat_dsim_dbs.pl  1.2  13 years  olson  Add license words.
reformat_fasta.pl  1.2  13 years  olson  Add license words.
reformat_sims.pl  1.8  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
reformat_timelogic_sims.pl  1.2  12 years  olson  rollup of changes for anno clearinghouse, RAST->SEED import.
register_features_batch.pl  1.2  13 years  olson  Add license words.
register_features_with_clearinghouse.pl  1.2  13 years  olson  Add license words.
register_genome_with_clearinghouse.pl  1.1  12 years  olson  Missing scripts.
rel2tabs.pl  1.1  13 years  overbeek  minor tools
relabel_nodes.pl  1.2  13 years  olson  Add license words.
relevant_PCHs.pl  1.3  13 years  olson  Add license words.
relevant_pchsG.pl  1.4  13 years  olson  Add license words.
remove_clustered_pchs.pl  1.10  12 years  overbeek  fix rfemove_clustered_PCHs to count correctly
remove_clustered_pchs2.pl  1.1  12 years  olson  Missing scripts.
remove_clustered_pchs3.pl  1.1  12 years  olson  Missing scripts.
remove_embedded_pegs.pl  1.17  11 years  gdpusch  Added setting of VERBOSE from metafile. -- /gdp
remove_rna_overlaps.pl  1.10  11 years  gdpusch  Added setting of VERBOSE from metafile. -- /gdp
remove_sims_not_in_nr.pl  1.1  12 years  olson  Missing scripts.
renumber_features.pl  1.11  11 years  gdpusch  Added option to print out ID map. -- /gdp
renumber_seed_dir.pl  1.2  13 years  olson  Add license words.
rep_genomes.pl  1.1  12 years  overbeek  fixes to representative tree generation and added rep_genomes
report_changes.pl  1.2  13 years  olson  Add license words.
representative_sequences.pl  1.4  12 years  golsen  Modifications to control ordering of sequences in representative sets and in seq...
representative_tree.pl  1.2  13 years  olson  Add license words.
reps_and_close.pl  1.2  12 years  overbeek  add make_trimmed_alignment_from_ids
restore_annotations.pl  1.2  13 years  olson  Add license words.
restore_assignments.pl  1.2  13 years  olson  Add license words.
restore_translation_rules.pl  1.2  13 years  olson  Add license words.
restrict_by_similarity.pl  1.4  13 years  olson  Add license words.
restrict_to_genomes.pl  1.3  13 years  olson  Add license words.
roles_in_subsystem.pl  1.2  13 years  olson  Add license words.
root_at.pl  1.2  13 years  olson  Add license words.
run_HMM_search_on_timelogic.pl  1.1  12 years  mkubal  version 1.0
run_fc.pl  1.2  13 years  olson  Add license words.
run_find_subsys_against_all_genomes.pl  1.2  12 years  overbeek  updates to computation of VCs
run_flux_optimization.pl  1.3  12 years  mkubal  error checking
run_glimmer2.pl  1.7  12 years  gdpusch  Added support for multiple genetic codes. -- /gdp
run_glimmer3.pl  1.3  11 years  gdpusch  Set paths to GLIMMER-3 and ELP from enviroment variables. -- /gdp
run_model_generation.pl  1.16  12 years  formsma  Added timestamp in GMT to the readme that is generated - Kevin
run_model_generation_all.pl  1.1  12 years  formsma  This script will generate models for all complete genomes in the seed. - Kevin
run_model_generation_v3.pl  1.2  12 years  mkubal  changed ouput to model_files.tgz
run_peg_job_worker.pl  1.4  13 years  olson  Add license words.
run_remote_PHOBIOUS.pl  1.1  12 years  mkubal  runs Phobius computation for given geneome
run_remote_Phobius_for_fasta.pl  1.1  11 years  mkubal  fasta file as input
run_remote_Phobius_for_genome.pl  1.1  12 years  mkubal  for single genome
run_remote_Phobius_for_genome_for_RAST.pl  1.1  12 years  mkubal  for use with RAST server
run_remote_Phobius_for_genomes.pl  1.1  12 years  mkubal  run for all complete prok genomes
run_scenarios.pl  1.3  12 years  formsma  Updated error statements to be correct - Kevin
run_start_predictions_for_all_subsystems.pl  1.4  13 years  olson  Add license words.
run_start_predictions_for_spreadsheet.pl  1.6  13 years  olson  Add license words.
runclustalw.pl  1.4  12 years  overbeek  add computation of alignments to building FIGFAMS
salvage_annotations.pl  1.6  13 years  olson  bugfix.
salvage_master_annotations.pl  1.3  13 years  overbeek  fixes to salvage code
salvage_subsystem_rows.pl  1.6  13 years  overbeek  fixes to salvage code
same_figfam.pl  1.2  12 years  overbeek  handle bad input in same_figfam
same_subsys.pl  1.1  13 years  overbeek  fixes to extract_genomes
score_dfcs.pl  1.3  13 years  overbeek  RAE: removing the header that should not be in the source
score_dfcs_mcauliffe.pl  1.5  13 years  overbeek  limit decimal positions in score
score_ifcs.pl  1.4  13 years  overbeek  RAE: More direct and indirect functional coupling scores
score_ifcs_mcauliffe.pl  1.2  13 years  overbeek  RAE: correcting indirect functional coupling score
seed2genbank.pl  1.3  12 years  olson  Tweak outptu file handling, expand '%g' into genome name. Allow diret output int...
seed2gff.pl  1.36  11 years  redwards  getting rid of need for strain info
seed2pir.pl  1.3  13 years  overbeek  RAE: moving PIRSF to links
seed_job_scheduler.pl  1.3  13 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
seed_run_task.pl  1.2  13 years  olson  readonly fixes; seed-run-job update to run from input file
select_genomes_for_sprout.pl  1.2  13 years  olson  Add license words.
sequence_length_histogram.pl  1.4  12 years  gdpusch  Rewrote counting of DNA characters (-get_dna option). -- /gdp
set_to_relation.pl  1.2  13 years  olson  Add license words.
show_reconfig_cmd.pl  1.3  13 years  olson  Add license words.
show_structured_english.pl  1.1  11 years  disz  Ross's code to generate annotations for NCBI
similar_to.pl  1.4  13 years  olson  Add license words.
sims_all.pl  1.5  12 years  overbeek  Added '-no_redo_blast' switch. -- /gdp
sims_between.pl  1.7  12 years  overbeek  updates on close connections
sketch_tree.pl  1.2  12 years  overbeek  add ability to insert sequences into a tree
sort_and_split_bbhs.pl  1.5  12 years  olson  add $ENV{SORT_ARGS} to sort invocations for running on large-memory machines
sp2fasta.pl  1.2  13 years  olson  Add license words.
split_and_install_pchs.pl  1.2  13 years  olson  Add license words.
split_and_trim_sequences.pl  1.14  12 years  overbeek  fix problem when repeats occur
split_assignments_based_on_subsystems.pl  1.1  13 years  overbeek  next version of the STAG code
split_by_genome.pl  1.1  13 years  overbeek  split_by_genome can be used to split a score or BBH file
split_clean_unclean_families.pl  1.4  13 years  overbeek  fixes for splitting families into clean/unclean
split_sims.pl  1.3  13 years  olson  Add license words.
splitup.pl  1.4  13 years  olson  Add license words.
sprout_search.pl  1.2  13 years  olson  Add license words.
start_data_for_set_of_pegs.pl  1.6  11 years  gdpusch  Added FIGV support. -- /gdp
start_dbserver.pl  1.2  13 years  olson  Add license words.
start_services.pl  1.12  13 years  olson  Add license words.
stop_services.pl  1.5  13 years  olson  Add license words.
submit_ff_test.pl  1.4  11 years  arodri7  update changes
submit_genome_to_rpsblast_against_CDD_on_biocluster.pl  1.2  12 years  mkubal  test for dir exist
submit_genome_to_signalP.pl  1.2  12 years  mkubal  test for dir exist
submit_to_iprscan_on_biocluster.pl  1.1  12 years  mkubal  run iprscan on cluster
subsys2pubmed.pl  1.4  12 years  hwang  change script to add new attribute after each subsystem versus after all subsyst...
subsys_info.pl  1.1  11 years  overbeek  subsys_info is subsystem information for Verionika
subtree_of.pl  1.2  13 years  olson  Add license words.
summarize_taxonomy_by_blast.pl  1.9  11 years  redwards  removing fatal error if 0 or 1 hits
sync_new_system.pl  1.6  13 years  golsen  Just adding a newline at end of file to make repository match my working copy. ...
synchronize_annotations_and_assignments.pl  1.2  13 years  olson  Add license words.
tabs2rel.pl  1.2  13 years  olson  Add license words.
test_Observation.pl  1.1  12 years  mkubal  for testing
test_cv.expected  1.1  13 years  efrank   Basic regression test on CV stuff at FIG API level (which underlies CGI).
test_cv.pl  1.2  13 years  olson  Add license words.
test_figfam_FF_peg.pl  1.3  11 years  olson  Missed one of the figfamdata fixes.
test_figfam_peg.pl  1.6  11 years  arodri7  update changes
test_figfam_placement_into_families.pl  1.9  11 years  olson  Introduct &FIG::get_figfams_data()
test_generate_anno_gff.pl  1.3  13 years  olson  Add license words.
test_parse_gff.pl  1.3  13 years  golsen  Don't mean to be pedantic, but I figured that I might as well add newlines at th...
test_placement.pl  1.1  11 years  overbeek  redone FIGfam stuff
tips_of.pl  1.3  12 years  overbeek  add insert_prot_into_tree, a new way to insert proteins into a tree
to_arabidopsis.pl  1.1  12 years  hwang  This script parses arabidopsis.org to get the AT aliases output
to_genbank.pl  1.4  12 years  gdpusch  Added support for multiple contig files. -- /gdp
to_gg.pl  1.2  13 years  olson  Add license words.
to_gids.pl  1.2  13 years  olson  Add license words.
to_insert.pl  1.2  13 years  olson  Add license words.
to_map_coords.pl  1.3  13 years  olson  Add license words.
to_org_specific.pl  1.4  13 years  hwang  fix syntax error
to_prodom.pl  1.6  13 years  hwang  Change url for prodom's post
to_structured_english.pl  1.1  11 years  overbeek  add routine to build structured english rendering of evidence codes
trace.pl  1.3  11 years  parrello  Fixed so that the destination is not case-sensitive.
track_figfams.pl  1.2  13 years  overbeek  get rid of diagnostics in track_figfams
translate.pl  1.2  13 years  olson  Add license words.
translation_of.pl  1.2  13 years  olson  Add license words.
trim_alignment.pl  1.2  12 years  overbeek  minor fixes
trim_sequences.pl  1.6  13 years  olson  Add license words.
trimmed_kernel_alignment.pl  1.1  12 years  overbeek  add last round of phylogeny tools
uni_lit_to_dlits.pl  1.1  11 years  overbeek  dlit support
uninstall.pl  1.2  13 years  olson  Add license words.
uninstall.sims.pl  1.2  13 years  olson  Add license words.
update-caches.pl  1.1  12 years  olson  Update SEED caches.
update_FIGfams.pl  1.10  11 years  arodri7  update changes
update_fr2go.pl  1.1  12 years  overbeek  put in the fr2go stuff
update_lineage.pl  1.3  11 years  wilke  draft version to update FIG taxonomy entries
update_nr_cycle.pl  1.6  13 years  overbeek  load ext org table on update_nr_cycle
update_sims.pl  1.13  13 years  olson  Add license words.
update_sims2.pl  1.4  11 years  olson  *** empty log message ***
update_taxonomies.pl  1.8  12 years  overbeek  set longer gap between accessing NCBI
update_uniq_id_data.pl  1.7  12 years  olson  use function_of_quick
uproot.pl  1.1  12 years  overbeek  add uproot
upstream.pl  1.3  13 years  olson  Add license words.
validate_fasta.pl  1.1  12 years  redwards  Initial release of programs to check and fix valid fasta format
validate_genome_gff.pl  1.6  13 years  olson  Add license words.
validate_subsystem.pl  1.2  13 years  olson  Add license words.
verify_genome_directory.pl  1.34  11 years  olson  Don't consider contigs.btree when looking for contigs.
verify_pegs_in_tbl.pl  1.2  13 years  olson  Add license words.
where_does_seq_hit.pl  1.2  13 years  olson  Add license words.

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