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File Rev. Age Author Last log entry
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html_parser.py  1.1  15 years  disz  Added html parser for picture making
build_nohit_fasta.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
cluster_objects.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
check_lost_sims.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
verify_pegs_in_tbl.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
blastn_seqs.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
break_scaffolds.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
load_pch_pins.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
check_for_unique_sims.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
blast_request.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
lengths_of_contigs.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
embl2gff_addmd5.py  1.1  14 years  efrank   # # embl2gff writes out a gff file that does not have the md5 sum in it. # I do...
install_translation_rules.pl  1.2  16 years  efrank  fixes to p2p
generate_pinned_homologs.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
apply_map.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
assess_completeness.pl  1.5  14 years  efrank   assess_completeness required the organism to be loaded in seed in order to run ...
install_lightweight_code.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
assign_with_no_sims.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
clean_sims.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
condense_blast.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
parse_mart.py  1.4  14 years  efrank   embl2gff- add ensembl protein id gff2seed- sort the fetaures before writing to ...
fix_eol.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
package_translation_rules.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
generate_similarities.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
package_lightweight_code.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
delete_genomes_from_sims.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
set_to_relation.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
restore_annotations.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
check_fast_sims.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
check_all_lost_sims.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
map_pegs.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
restore_assignments.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
assign.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
reformat_dsim_dbs.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
embl2gff.pl  1.17  14 years  efrank   embl2gff- add ensembl protein id gff2seed- sort the fetaures before writing to ...
bring_system_up_to_date.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
build_access_sets.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
generate_input_for_auto_assignments.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
check_tbl.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
uninstall.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
package_code.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
uninstall.sims.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
check_changes_in_organisms.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
fasta_for_hypo.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
README  1.1.1.1  16 years  efrank   import
put_directory_in_one_file.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
make_binary.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
restore_translation_rules.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
gff2seed.pl  1.18  14 years  efrank   embl2gff- add ensembl protein id gff2seed- sort the fetaures before writing to ...
make_occ_counts.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
install_code.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
list_genomes.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
rationalize_blast.pl  1.2  16 years  efrank   fixed a bunch of changes
load_chromosomal_clusters.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
backup_subsystems.pl  1.1  16 years  gdpusch  Script to back up the "Data/Subsystems/" directory. -- /gdp
splitup.pl  1.3  15 years  gdpusch  Added error-checking.
make_transferable_chunks.pl  1.3  15 years  gdpusch  Added error-checking.
genome_peg_dna.pl  1.1  15 years  golsen  Tool to dump peg DNA sequences
align_fasta.pl  1.1  15 years  golsen  add_to_alignment FastaAlignment FastaSeqs > NewFastaAlignment - Add new seque...
clustal2fasta.pl  1.1  15 years  golsen  add_to_alignment FastaAlignment FastaSeqs > NewFastaAlignment - Add new seque...
add_to_alignment.pl  1.1  15 years  golsen  add_to_alignment FastaAlignment FastaSeqs > NewFastaAlignment - Add new seque...
roles_in_subsystem.pl  1.1  15 years  golsen  *** empty log message ***
fastasize.c  1.1  15 years  golsen  assess_completeness reads the contigs in one or more specified genome directorie...
make_attribute_index.pl  1.5  14 years  mkubal  transaction_log no longer included in attribute.index
get_pathways_for_EC.pl  1.1  16 years  mkubal  get pathways from KEGG
cat_spreadsheet.pl  1.1  16 years  mkubal  cat_spreadsheet.pl w/o header
make_indexes.pl  1.10  14 years  mkubal  make phage and pi searchable
fig_net.pl  1.2  16 years  mkubal  script to get ECs with no genes
get_empty_ecs.pl  1.3  16 years  mkubal  change to EF dir
get_empty_ecs  1.2  16 years  mkubal  6-22 version of get_empty_ecs
fig_rpc.pl  1.2  16 years  mkubal  script to get ECs with no genes
fig_xmlrpc_server.pl  1.4  16 years  mkubal  script to get ECs with no genes
cat_spreadsheet  1.2  16 years  mkubal  script to get ECs with no genes
export_subsystem_as_gff.pl  1.1  15 years  olson  script to write a subsystem as a set of gff files + a spreadsheet.
relevant_pchsG.pl  1.3  14 years  olson  Fixes for coupling scripts.
compute_new_ids.pl  1.1  16 years  olson  new app for doing updates
generate_Property_for_sprout.pl  1.5  15 years  olson  More property fixes.
package_annotations.pl  1.8  14 years  olson  Make annotations_made_fast return new Annotation objects instead of arrays of da...
boot_cluster_seed.pl  1.3  14 years  olson  fixes to clster bootup script
show_reconfig_cmd.pl  1.2  15 years  olson  add sprout db support.
register_features_with_clearinghouse.pl  1.1  14 years  olson  New script to register feature IDs with the clearinghouse.
index_contig_files.c  1.2  15 years  olson  Add support for computing MD5 checksums for contigs and genomes. The checksum o...
md5.c  1.1  15 years  olson  Add support for computing MD5 checksums for contigs and genomes. The checksum o...
sprout_search.pl  1.1  15 years  olson  simple cmd interface to sprout search
init_peg_job_scheduler.pl  1.3  15 years  olson  New jobsched stuff.
postprocess_computed_sims.pl  1.1  15 years  olson  Scrript to do final postprocessing of sims files.
synchronize_annotations_and_assignments.pl  1.1  14 years  olson  Generate an annotation file and an assignment file that when installed will brin...
validate_subsystem.pl  1.1  15 years  olson  Basic subsystem package validator. Uses SubsystemFile from P2Pupdate module.
validate_genome_gff.pl  1.5  14 years  olson  Don't join the contigs.
make_close.pl  1.3  15 years  olson  Create mapped gnum/pnum pairs instead of fig ids on output.
test_generate_anno_gff.pl  1.2  15 years  olson  Updates to GFF stuff.
make_transferable_tarfiles.pl  1.2  15 years  olson  Make GBrowse work with new Sprout changes.
stop_services.pl  1.4  15 years  olson  Some small fixes.
seed_job_scheduler.pl  1.2  15 years  olson  More subsystem/p2p fixes.
index_translations.pl  1.14  15 years  olson  Use tac for file reverse on solaris too.
extend_subsystem.pl  1.1  16 years  olson  add extend_susbsystem script
package_sims.pl  1.1  14 years  olson  Add sims packager.
start_dbserver.pl  1.1  15 years  olson  database server manipulation scripts.
renumber_seed_dir.pl  1.1  14 years  olson  Script to change the genome id for a genome directory.
load_sims.pl  1.7  14 years  olson  Add table size estimation code for supporting MyISAM.
fasta_cksum.c  1.2  15 years  olson  Remove ^Ms
peg_to_pdb.py  1.1  15 years  olson  New script for creating pseudo-pdb files from a peg in the seed.
export_similarity_request.pl  1.1  15 years  olson  Script to invoke sim request export.
blastp_pseq.pl  1.3  15 years  olson  Use the proper BLASTMAT location.
dump_machine_state.pl  1.2  14 years  olson  Wider ps.
assign_synonym_ids.pl  1.1  14 years  olson  Scripts for assigning xxx numbers to peg.syn and friends.
make_maps_from_sub.py  1.4  16 years  olson  test for existence of link before referring to it.
run_peg_job_worker.pl  1.3  15 years  olson  New jobsched stuff.
map_sims_for_bigfc.pl  1.1  15 years  olson  Updated tools for functional coupling computation. Replace string pges with (gen...
index_subsystems.pl  1.6  14 years  olson  Careful cleanup of subsystem indexing. Patched a bunch of spots where needed upd...
init_dbserver.pl  1.2  15 years  olson  pass requried argument down to call.
index_translation_files.c  1.1  15 years  olson  Gary Olsen's optimized database loading code. This probably needs to be tweaked...
p2p_sync_cron.pl  1.2  15 years  olson  fix typos.
export_genome_as_gff.pl  1.5  14 years  olson  Make annotations_made_fast return new Annotation objects instead of arrays of da...
compute_contig_md5.pl  1.2  15 years  olson  Tidy it up.
start_services.pl  1.11  15 years  olson  remove debug
das_test.pl  1.1  15 years  olson  das server test script
load_coupling.pl  1.6  14 years  olson  Add table size estimation code for supporting MyISAM.
assign_synonym_ids_to_sims.pl  1.1  14 years  olson  Scripts for assigning xxx numbers to peg.syn and friends.
p2p_daemon.pl  1.1  15 years  olson  standalone daemon for querying for relayed soap requests
test_parse_gff.pl  1.1  15 years  olson  GFF parsing/generation test scripts.
package_assignments.pl  1.7  16 years  olson  add usage message
make_sim_tab.pl  1.5  15 years  olson  Create mapped gnum/pnum pairs instead of fig ids on output.
index_sims_file.c  1.1  15 years  olson  Gary Olsen's optimized database loading code. This probably needs to be tweaked...
register_features_batch.pl  1.1  14 years  olson  Register a batch of IDs.
install-data.pl  1.6  15 years  olson  Fixed up installer.
backup_critical_data.pl  1.3  15 years  olson  Don't backup the annotations in the NR, they're huge and readonly.
reduce_sims.pl  1.8  15 years  olson  added some comments
p2p_sync_from_remote.pl  1.3  15 years  olson  Add support for passing credentials via a file so they're not on the cmdline in ...
load_close.pl  1.6  14 years  olson  Fixes for coupling scripts.
compute_sim_chunk.pl  1.1  15 years  olson  Start local sim compuation.
assign_synonym_ids_to_nr.pl  1.1  14 years  olson  Scripts for assigning xxx numbers to peg.syn and friends.
import_subsystems.pl  1.21  14 years  olson  Make import_subsystems use the P2PUpdate::SubsystemFile code for parsing subsyst...
load_local_maps.pl  1.2  16 years  olson  Clean up map support.
peg_to_name.pl  1.3  16 years  olson  Some tweaks.
function_of.pl  1.3  15 years  overbeek  add new subsystem interface
make_ncbi_files.pl  1.1  14 years  overbeek  Process NCBI data for addition to the NR. -- /gdp
run_start_predictions_for_all_subsystems.pl  1.3  14 years  overbeek  fixes to call_starts
exclude_genomes.pl  1.1  16 years  overbeek  Converse of `extract_genomes` --- takes list of genomes to exclude. -- /gdp
count_bases.pl  1.1  15 years  overbeek  add tree manipulation utilities
check_starts_for_pegs.pl  1.3  14 years  overbeek  Minor cosmetic changes
fill_in_roles.pl  1.3  15 years  overbeek  clean up of auto assignments routines
index_annotations.pl  1.8  14 years  overbeek  fixes to update_uniq_id_data
update_sims.pl  1.12  14 years  overbeek  fixes to update_uniq_id_data
is_prokaryotic.pl  1.1  15 years  overbeek  lots of data mining stuff
get_class_examples.pl  1.1  15 years  overbeek  add program to generate class challenge problems
split_sims.pl  1.2  15 years  overbeek  Modified to take input from either STDIN or files; added more informative error-...
install_assignments.pl  1.6  15 years  overbeek  sort links
make_subsystems_from_clusters.pl  1.4  15 years  overbeek  fixes to generation of subsystems from clusters
sp2fasta.pl  1.1  14 years  overbeek  Program to extract FASTA files from SwissProt/TrEMBL/UniProt .dat files. -- /gdp...
changed_starts.pl  1.6  14 years  overbeek  fixes to calling starts
order_sets.pl  1.2  14 years  overbeek  add assign_to_sets
filter_pegs_in_subsystems.pl  1.3  15 years  overbeek  clean up of auto assignments routines
extract_data_for_syncing_after_update.pl  1.5  16 years  overbeek  package outputs from extract_data_for_syncing_after_update into a directory
clean_subsystems.pl  1.1  15 years  overbeek  add clean_subsystems
dna_seq.pl  1.1  16 years  overbeek  interval stuff
load_links.pl  1.5  15 years  overbeek  add make_sprout_upstream
build_alignments_for_subsystems.pl  1.3  15 years  overbeek  add assign_using_tree and fix overlays in pinned regions
run_start_predictions_for_spreadsheet.pl  1.5  14 years  overbeek  fixes to starts
connections_between.pl  1.1  15 years  overbeek  connections_between got added
sims_between.pl  1.1  15 years  overbeek  add computation of similarities - sims_all and sims_between - between close stra...
assign_to_unchanged.pl  1.1  15 years  overbeek  major change to BBHs (use precomputed)
filter_tbl_overlaps.pl  1.6  14 years  overbeek  fixes to computing starts
get_nr_entries_without_sims.pl  1.3  14 years  overbeek  fixes to update_uniq_id_data
split_and_install_pchs.pl  1.1  14 years  overbeek  Install PCHs to per-genome files.
generate_GenomeGroups_for_sprout.pl  1.2  14 years  overbeek  fixes to showing reactions
build_nr_sources.pl  1.6  15 years  overbeek  Modified to exclude environmental samples. -- /gdp
check_subsystems.pl  1.3  15 years  overbeek  add checking for subsystems
reformat_contigs.pl  1.1  14 years  overbeek  Script to standardize FASTA format contig files; also splits scaffolds into cont...
questionable_calls.pl  1.1  15 years  overbeek  minor improvements to automated assignments
select_genomes_for_sprout.pl  1.1  15 years  overbeek  add select_genomes_for_sprout
cluster_by_sim.pl  1.1  16 years  overbeek  add cluster_by_sim
add_rbs_data_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
bbhs.pl  1.6  15 years  overbeek  major change to BBHs (use precomputed)
compute_pins_and_clusters.pl  1.1  16 years  overbeek  added pins and clusters properly
db_xrefs_of.pl  1.3  15 years  overbeek  fixes to db_xrefs
external_calls.pl  1.1  15 years  overbeek  minor improvements to automated assignments
update_uniq_id_data.pl  1.5  14 years  overbeek  fixes to update_uniq_id_data
compute_simple_scores.pl  1.3  15 years  overbeek  fixes to computing coupling scores
make_sp_func_syn_dicts.pl  1.1  14 years  overbeek  Extract function data from SwissProt/TrEMBL/UniProt .dat files. -- /gdp
remove_clustered_pchs.pl  1.6  14 years  overbeek  NMPDR updates.
pegs_in_conflict.pl  1.2  15 years  overbeek  add clean_subsystems
order_corrections_for_start_predictions.pl  1.3  14 years  overbeek  fixes to calling starts
insert_all.pl  1.1  15 years  overbeek  add tree manipulation utilities
run_fc.pl  1.1  15 years  overbeek  add routines for BigFC
check_alignment.pl  1.1  15 years  overbeek  add tree manipulation utilities
get_fasta_for_tbl_entries.pl  1.4  15 years  overbeek  Modified to handle included terminal STOP codons. -- /gdp
add_sim_data_for_start_predictions.pl  1.6  14 years  overbeek  fixes to computing starts
apply_peg_changes_to_subsystem.pl  1.2  14 years  overbeek  NMPDR updates.
seed2gff.pl  1.10  14 years  overbeek  Updating seed2gff.pl to validate against IOWG
ali_to_seq.pl  1.1  15 years  overbeek  add tree manipulation utilities
relabel_nodes.pl  1.1  15 years  overbeek  add tree manipulation utilities
all_subsystems.pl  1.1  15 years  overbeek  filters for data mining
location_of.pl  1.1  15 years  overbeek  filters for data mining
sync_new_system.pl  1.4  15 years  overbeek  sort links
split_and_trim_sequences.pl  1.9  15 years  overbeek  fix to split_and_trim
make_sp_uni_files.pl  1.1  14 years  overbeek  Master driver to parse SwissProt/TrEMBL/UniProt .dat files for NR. -- /gdp
process_sim_deletions_and_replacements.pl  1.2  15 years  overbeek  various fixes to package/install annotations
make_match_table.pl  1.1  16 years  overbeek  up max size of bbh extras
restrict_by_similarity.pl  1.3  16 years  overbeek  fix to restrict_by_similarity
aliases_of.pl  1.5  15 years  overbeek  fixes to aliases_of and added potentially_cotranscribed
make_PHOBs_for_subsystems.pl  1.4  15 years  overbeek  add tool to generate gene blocks for variation analysis
check_peg_assignments.pl  1.2  15 years  overbeek  support checking assignments in subsystems
load_attributes.pl  1.26  14 years  overbeek  correcting \r error
make_assignments_set.pl  1.2  15 years  overbeek  Ross change commit after cleanup
similar_to.pl  1.3  15 years  overbeek  add error stream for hits as tool runs in similar_to
initial_set.pl  1.1  15 years  overbeek  added two phylogeny tools
get_dna.pl  1.2  15 years  overbeek  Modified to read from either a file or STDIN. -- /gdp
extract_DNA_sequence_from_object_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
build_nr.pl  1.11  14 years  overbeek  fixes to update_uniq_id_data
get_sims_for_start_predictions.pl  1.3  14 years  overbeek  Minor cosmetic changes
alter_tbl.pl  1.3  14 years  overbeek  Converted from "in-place" to "filter" action. -- /gdp
merge_translation_rules.pl  1.6  16 years  overbeek  fix translation rules
reformat_sims.pl  1.5  14 years  overbeek  adding other fasta files to reformat sims
map_sims.pl  1.4  15 years  overbeek  map_sims handles both remapping and deleted
get_translations.pl  1.1  15 years  overbeek  add get_translations
fasta_to_phylip.pl  1.1  15 years  overbeek  lots of data mining stuff
upstream.pl  1.2  15 years  overbeek  lots of data mining stuff
cluster_by_bbhs.pl  1.1  16 years  overbeek  more data mining tools
root_at.pl  1.1  15 years  overbeek  add tree manipulation utilities
assign_to_hypo.pl  1.2  16 years  overbeek  fixes in auto assignments
import_external_sequences_step3.pl  1.4  15 years  overbeek  still trying to get the import of external sources right
tips_of.pl  1.1  15 years  overbeek  add tree manipulation utilities
project.pl  1.1  15 years  overbeek  add simple tool to investigation of projection
alias2fig.pl  1.1  16 years  overbeek  initial alias2fig
tabs2rel.pl  1.1  15 years  overbeek  add tool to generate gene blocks for variation analysis
verify_genome_directory.pl  1.24  14 years  overbeek  Minor change in diagnostic statement. -- gdp
is_archaeal.pl  1.1  15 years  overbeek  lots of data mining stuff
generate_Source_for_sprout.pl  1.1  15 years  overbeek  routines to support derivation of sprout data
extract_genes.pl  1.4  14 years  overbeek  fixes to starts
extract_sp_links.pl  1.1  14 years  overbeek  Extract PubMed links from SwissProt/TrEMBL/UniProt .dat files. -- /gdp
make_fig_files.pl  1.1  15 years  overbeek  updates to build protein families
adjacent.pl  1.1  16 years  overbeek  interval stuff
make_sprout_upstream.pl  1.1  15 years  overbeek  add make_sprout_upstream
keep_only.pl  1.1  15 years  overbeek  add keep_only
make_sp_org_domain_table.pl  1.1  14 years  overbeek  Create org.table from SwissProt/TrEMBL/UniProt .dat files. -- /gdp
expand_multifunctional_roles.pl  1.2  15 years  overbeek  add make_spreadsheet_and_notes
assign_to_close_strains.pl  1.6  15 years  overbeek  clean up of auto assignments routines
peg_to_subsystems.pl  1.2  15 years  overbeek  minor updates to peg_to_subsystems
generate_gene_blocks.pl  1.2  14 years  overbeek  Minor cosmetic changes
predict_starts.pl  1.6  14 years  overbeek   fixes to pick_gene_boundaries
start_data_for_set_of_pegs.pl  1.3  14 years  overbeek  Minor cosmetic changes
to_insert.pl  1.1  15 years  overbeek  added two phylogeny tools
make_phob_from_ids.pl  1.2  15 years  overbeek  Translate selenocystein chars to "X". -- /gdp
fill_in_cell.pl  1.1  15 years  overbeek  fill_in_cell for Heiko
make_kegg_files.pl  1.1  14 years  overbeek  Process KEGG data for addition to the NR. -- /gdp
genbank2gff3.pl  1.4  14 years  overbeek  minor bug fix on ids
paint_tree.pl  1.2  15 years  overbeek  generalize paint_tree to handle newick trees
make_sp_org_table.pl  1.1  14 years  overbeek  Create org.table from SwissProt/TrEMBL/UniProt .dat files. -- /gdp
potentially_cotranscribed.pl  1.1  15 years  overbeek  fixes to aliases_of and added potentially_cotranscribed
possibly_truncated.pl  1.1  15 years  overbeek  add update_subsys_conflicts to fig.pl
fill_subsys.pl  1.4  15 years  overbeek  make fill_subsys set user correctly
install_subsystems.pl  1.1  16 years  overbeek  p2p changes
match_dna_to_aligned_prots.pl  1.3  15 years  overbeek  changes to calling starts code
make_close_strain_data.pl  1.9  14 years  overbeek  Minor cosmetic changes. -- /gdp
compare_tree_and_alignment.pl  1.1  15 years  overbeek  add tree manipulation utilities
check_nr_and_peg_synonyms.pl  1.1  15 years  overbeek  Initial check-in -- /gdp
fid2dna.pl  1.1  16 years  overbeek  add pegs and fid2dna
find_maximal_clusters.pl  1.1  15 years  overbeek  add find_maximal_clusters
pull_sp_entries.pl  1.1  14 years  overbeek  Extract entries matching a pattern from SwissProt/TrEMBL/UniProt .dat files. -- ...
get_ev_codes.pl  1.3  14 years  overbeek  add evidence codes to protein.cgi
best_hits.pl  1.1  15 years  overbeek  add tree manipulation utilities
fusion_of.pl  1.1  16 years  overbeek  add fusion_of
interval.pl  1.1  16 years  overbeek  interval stuff
runclustalw.pl  1.2  15 years  overbeek  make runclustalw handle embedded stops
load_features.pl  1.19  14 years  overbeek  fixes to load_features for duplicate tbl entries
trim_sequences.pl  1.5  15 years  overbeek  use neighbor joining, not fitch, to build trees
build_initial_objects_for_start_predictions.pl  1.7  14 years  overbeek  fixes to bugs in calling starts
get_long_enough.pl  1.1  15 years  overbeek  add tree manipulation utilities
make_sp_desc_with_org.pl  1.1  14 years  overbeek  Extract description and organism data lines from SwissProt/TrEMBL/UniProt .dat f...
pegs_in_subsystem.pl  1.4  15 years  overbeek  add pegs_in_conflict
bielefeld_tarfile_to_seed.pl  1.1  14 years  overbeek  Processes a Bielefeld gene-call tarfile to produce a SEED skeleton directory. --...
install_annotations.pl  1.3  16 years  overbeek  attempt to fix package/install for p2p
sort_and_split_bbhs.pl  1.3  14 years  overbeek  fixes in BBH generation
install_feature_updates.pl  1.1  15 years  overbeek  fix by_variant and by_pattern sort codes in subsys.cgi
is_eukaryotic.pl  1.1  15 years  overbeek  lots of data mining stuff
make_assignments_fit_initial_css.pl  1.3  15 years  overbeek  fixes to generation of subsystems from clusters
build_syn.pl  1.1  15 years  overbeek  updates to build protein families
extract_subset_from_sprout_data.pl  1.1  15 years  overbeek  add ability to extract subsets of sprout data
add_start_data_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
check_sims_basic.pl  1.6  15 years  overbeek  minor fix to phylogernetic profiles
add_assignments.pl  1.2  16 years  overbeek  fix add_assignments
generate_sprout_links.pl  1.1  15 years  overbeek  add generate_sprout_links
gi2fig.pl  1.2  16 years  overbeek  minor fix to gi2fig
package_subsystems.pl  1.3  16 years  overbeek  p2p changes
restrict_to_genomes.pl  1.2  16 years  overbeek  more data mining tools
translate.pl  1.1  16 years  overbeek  add a minimal translation utility
conditionally_assign.pl  1.2  15 years  overbeek  add check to assign_function
make_spreadsheet_and_notes.pl  1.2  15 years  overbeek  fixes to generation of subsystems from clusters
functionally_coupled.pl  1.4  15 years  overbeek  automatically generate aliases from mapped IDs
Makefile  1.17  14 years  overbeek  Added rule for "fastasize.c"
load_protein_families.pl  1.6  14 years  overbeek  update stuff relating to protein families
make_sim_sets.pl  1.2  16 years  overbeek  fixes from G5 at Fonsteins
blast2gff.pl  1.8  14 years  overbeek  changing ends calculation
get_best_set_of_genes_for_column.pl  1.2  15 years  overbeek  allow set of seeks to cores for bbhs
generate_intergenic_blocks.pl  1.2  15 years  overbeek  fix to generate_intergenic_blocks
get_potential_starts_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
to_gids.pl  1.1  16 years  overbeek  utility to convert FIG ids to GI ids
extract_DNA_for_whole_ORFs.pl  1.2  14 years  overbeek  fixes to computing starts
clustal_to_fasta.pl  1.1  15 years  overbeek  add clustal_to_fasta
index_fasta.pl  1.1  15 years  overbeek  add tree manipulation utilities
assign_to_sets.pl  1.4  14 years  overbeek  fixes to starts
filter_new_overlaps.pl  1.1  14 years  overbeek  modified version of `filter_tbl_overlaps.pl`, used when sets of orthologs have b...
pull_fasta_entries.pl  1.5  14 years  overbeek  fixes to update_uniq_id_data
subtree_of.pl  1.1  15 years  overbeek  add subtree_of
merge_annotations.pl  1.2  15 years  overbeek  additions for sprout
all_bbhs.pl  1.2  14 years  overbeek  fixes in BBH generation
genomes_of.pl  1.1  16 years  overbeek  basic query tools
expand_blast_table.pl  1.1  16 years  overbeek  remember, .pl
compute_changed_ids_for_nrs.pl  1.3  14 years  overbeek  fixes to update_uniq_id_data
pull_orfs.pl  1.2  16 years  overbeek  use FIG in pull_orfs
check_starts_for_peg_sets.pl  1.4  14 years  overbeek  Minor cosmetic changes
is_bacterial.pl  1.1  15 years  overbeek  lots of data mining stuff
make_protein_sets.pl  1.3  16 years  overbeek  Fixed out-of-mempoy error by replacing backticked grep through NR with pipe-open...
translation_of.pl  1.1  16 years  overbeek  add aliases_of and translation_of filters
update_taxonomies.pl  1.6  16 years  overbeek  Converted from "wget" to "curl"
make_phob_from_seqs.pl  1.6  15 years  overbeek  fixes to using trees under subsystems
make_sprout_bbhs.pl  1.1  14 years  overbeek  Sprout BBH generator.
make_fam_tabs.pl  1.2  14 years  overbeek  update stuff relating to protein families
pegs.pl  1.2  16 years  overbeek  interval stuff
check_sims_syntax.pl  1.2  14 years  overbeek  Minor cosmetic change. -- /gdp
auto_assign.pl  1.14  14 years  overbeek  fixes to update_uniq_id_data
prep_viz.pl  1.1  15 years  overbeek  add start prediction code
extract_data_to_keep.pl  1.4  15 years  overbeek  allow -v on extract_data_to_keep
fig_specific_sequences.pl  1.1  15 years  overbeek  add fig_specific_sequences
mark_nr.pl  1.1  16 years  overbeek  up max size of bbh extras
insert.pl  1.1  15 years  overbeek  add tree manipulation utilities
parse_genbank.pl  1.11  14 years  overbeek  Fixed bug in function-parsing logic. -- /gdp
reformat_fasta.pl  1.1  14 years  overbeek  Script to standardize FASTA format files. -- /gdp
make_rates.pl  1.1  15 years  overbeek  add tree manipulation utilities
import_external_sequences_step1.pl  1.7  15 years  overbeek  current external update procedure set
pp.pl  1.2  15 years  overbeek  minor fix to phylogernetic profiles
generate_max_clusters.pl  1.1  15 years  overbeek  add program to generate maximal clusters
extend_subsys.pl  1.5  15 years  overbeek  fix error on passing user to index.cgi -- header fix
compute_potential_fusions.pl  1.6  16 years  overbeek  change similarity threshold for computing fusions
build_excel_gene_table.pl  1.2  16 years  overbeek  fix build_excel_gene_table
generate_kernel_css.pl  1.4  15 years  overbeek  fixes to generate_kernet_css
expand_transferred_chunks.pl  1.3  16 years  overbeek  fix pattern in expand_transferred_chunks
load_kegg.pl  1.5  14 years  overbeek  fix to HOPSS.cgi
make_calls.pl  1.3  15 years  overbeek  cleaned up auto_assign
extract_genomes.pl  1.27  14 years  overbeek  make Sprout optional in sigs.cgi
process_new_sims.pl  1.2  15 years  overbeek  Significant changes to syntax and structure. -- /gdp
representative_tree.pl  1.1  15 years  overbeek  add tree manipulation utilities
relevant_PCHs.pl  1.2  14 years  overbeek  NMPDR updates.
generate_subsys_tables_for_sprout.pl  1.7  15 years  overbeek  fixes to Sprout Data generation
build_exemplar_fasta.pl  1.2  16 years  overbeek  fixes from G5 at Fonsteins
align_with_clustal.pl  1.7  15 years  overbeek  minor fixes to alignments
fix_ext_funcs.pl  1.1  15 years  overbeek  routines to support derivation of sprout data
make_calls_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
pegs_in_subsystems.pl  1.3  15 years  overbeek  add trim_sequences
sims_all.pl  1.1  15 years  overbeek  add computation of similarities - sims_all and sims_between - between close stra...
build_alignments_from_spreadsheet.pl  1.5  15 years  overbeek  minor fixes to alignments
build_protein_families.pl  1.2  14 years  overbeek  add get_ev_codes
generate_pin_caches.pl  1.4  15 years  overbeek  fixes to generate_pin_caches
distribute_attributes.pl  1.9  14 years  overbeek  Checking number of columns
format_peg_dbs.pl  1.2  15 years  parrello  *** empty log message ***
index_sprout.pl  1.11  14 years  parrello  *** empty log message ***
load_bbhs.pl  1.11  15 years  parrello  Converted to use the "reload_table" methods. These determine whether or not it i...
load_external_orgs.pl  1.2  15 years  parrello  *** empty log message ***
load_sets.pl  1.4  15 years  parrello  *** empty log message ***
fix_annotations.pl  1.1  14 years  parrello  Added to fix malformed annotations.
load_ec_names.pl  1.3  15 years  parrello  *** empty log message ***
NMPDRAnalysis.pl  1.2  14 years  parrello  Fixed the documentation.
generate_genome_feature_tables_for_sprout.pl  1.15  14 years  parrello  Accidentally removed a useless tab.
load_distances.pl  1.4  15 years  parrello  *** empty log message ***
index_sims.pl  1.8  15 years  parrello  *** empty log message ***
Simple.pl  1.2  14 years  parrello  Fixed documentation.
TransactFeatures.pl  1.15  14 years  parrello  Fixed documentation. Added back the ability to generate TBL output files.
TestLocations.pl  1.4  14 years  parrello  *** empty log message ***
compute_genome_counts.pl  1.12  15 years  parrello  *** empty log message ***
load_literature.pl  1.2  15 years  parrello  *** empty log message ***
init_maps.pl  1.2  15 years  parrello  *** empty log message ***
init_FIG.pl  1.6  15 years  parrello  *** empty log message ***
load_peg_mapping.pl  1.5  15 years  parrello  *** empty log message ***
index_neighborhoods.pl  1.2  15 years  parrello  *** empty log message ***
index_contigs.pl  1.10  15 years  parrello  *** empty log message ***
make_annotations_for_sprout.pl  1.11  14 years  parrello  Updated indenting.
add_assertions_of_function.pl  1.27  14 years  parrello  *** empty log message ***
Packager.pl  1.3  14 years  parrello  Fixed documentation.
load_sprout.pl  1.32  14 years  parrello  Added better error handling to the "-index" option.
assign_towards_subsystems.pl  1.1  14 years  redwards  Initial release of a more relaxed assignment script. Prefers (with limits) to pu...
complete_genomes.pl  1.6  15 years  redwards  changed tag/value pairs completely. Ooops!
seed2pir.pl  1.1  15 years  redwards  adding batch command for making seed2pir comparisons
gather_attributes.pl  1.6  14 years  redwards  Fixing bugz #156
display_tree.pl  1.3  15 years  redwards  changing displaytree
load_pirsf.pl  1.8  14 years  redwards  load_pirsf attributes
dump_attributes.pl  1.1  14 years  redwards  Updating attributes code
fig.pl  1.83  14 years  redwards  adding differentiate protein families

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