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File Rev. Age Author Last log entry
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ComputeSproutCouplings.pl  1.1.2.1  14 years  olson  Merged from trunk.
Makefile  1.16  14 years  efrank   this, combined with head for ReleaseTools should do reasonable thing for .c cod...
README  1.1.1.1  16 years  efrank   import
Simple.pl  1.1  14 years  parrello  *** empty log message ***
add_assertions_of_function.pl  1.24.2.1  14 years  olson  Merged from trunk.
add_assignments.pl  1.2  15 years  overbeek  fix add_assignments
add_rbs_data_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
add_sim_data_for_start_predictions.pl  1.2  14 years  overbeek  add tool to generate gene blocks for variation analysis
add_start_data_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
add_to_alignment.pl  1.1  14 years  golsen  add_to_alignment FastaAlignment FastaSeqs > NewFastaAlignment - Add new seque...
adjacent.pl  1.1  15 years  overbeek  interval stuff
ali_to_seq.pl  1.1  15 years  overbeek  add tree manipulation utilities
alias2fig.pl  1.1  15 years  overbeek  initial alias2fig
aliases_of.pl  1.5  15 years  overbeek  fixes to aliases_of and added potentially_cotranscribed
align_fasta.pl  1.1  14 years  golsen  add_to_alignment FastaAlignment FastaSeqs > NewFastaAlignment - Add new seque...
align_with_clustal.pl  1.7  14 years  overbeek  minor fixes to alignments
all_bbhs.pl  1.1.2.1  14 years  olson  Merged from trunk.
all_subsystems.pl  1.1  14 years  overbeek  filters for data mining
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  1.3  14 years  overbeek  fixes to start predictions
assign.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
assign_to_close_strains.pl  1.6  14 years  overbeek  clean up of auto assignments routines
assign_to_hypo.pl  1.2  15 years  overbeek  fixes in auto assignments
assign_to_unchanged.pl  1.1  14 years  overbeek  major change to BBHs (use precomputed)
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...
auto_assign.pl  1.13  14 years  overbeek  clean up of auto assignments routines
backup_critical_data.pl  1.3  14 years  olson  Don't backup the annotations in the NR, they're huge and readonly.
backup_subsystems.pl  1.1  15 years  gdpusch  Script to back up the "Data/Subsystems/" directory. -- /gdp
bbhs.pl  1.6  14 years  overbeek  major change to BBHs (use precomputed)
best_hits.pl  1.1  15 years  overbeek  add tree manipulation utilities
blast_request.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...
blastp_pseq.pl  1.3  15 years  olson  Use the proper BLASTMAT location.
boot_cluster_seed.pl  1.2  14 years  olson  Updates.
break_scaffolds.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
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...
build_alignments_for_subsystems.pl  1.3  15 years  overbeek  add assign_using_tree and fix overlays in pinned regions
build_alignments_from_spreadsheet.pl  1.5  14 years  overbeek  minor fixes to alignments
build_excel_gene_table.pl  1.2  16 years  overbeek  fix build_excel_gene_table
build_exemplar_fasta.pl  1.2  16 years  overbeek  fixes from G5 at Fonsteins
build_initial_objects_for_start_predictions.pl  1.3  14 years  overbeek  add tool to generate gene blocks for variation analysis
build_nohit_fasta.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
build_nr.pl  1.7  14 years  overbeek  untested import_external_sequences_step1
build_nr_sources.pl  1.6  14 years  overbeek  Modified to exclude environmental samples. -- /gdp
cat_spreadsheet  1.2  15 years  mkubal  script to get ECs with no genes
cat_spreadsheet.pl  1.1  15 years  mkubal  cat_spreadsheet.pl w/o header
check_alignment.pl  1.1  15 years  overbeek  add tree manipulation utilities
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...
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...
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_for_unique_sims.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...
check_peg_assignments.pl  1.2  15 years  overbeek  support checking assignments in subsystems
check_sims_basic.pl  1.5  14 years  overbeek  add process_sim_deletions_and_replacements
check_starts_for_peg_sets.pl  1.1  14 years  overbeek  minor fixes in computing functional coupling
check_subsystems.pl  1.3  15 years  overbeek  add checking for subsystems
check_tbl.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...
clean_subsystems.pl  1.1  14 years  overbeek  add clean_subsystems
clustal2fasta.pl  1.1  14 years  golsen  add_to_alignment FastaAlignment FastaSeqs > NewFastaAlignment - Add new seque...
clustal_to_fasta.pl  1.1  15 years  overbeek  add clustal_to_fasta
cluster_by_bbhs.pl  1.1  15 years  overbeek  more data mining tools
cluster_by_sim.pl  1.1  15 years  overbeek  add cluster_by_sim
cluster_objects.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
compare_tree_and_alignment.pl  1.1  15 years  overbeek  add tree manipulation utilities
complete_genomes.pl  1.6  14 years  redwards  changed tag/value pairs completely. Ooops!
compute_changed_ids_for_nrs.pl  1.2  14 years  overbeek  Modified syntax and structure to eliminate mapping step. -- /gdp
compute_contig_md5.pl  1.2  14 years  olson  Tidy it up.
compute_genome_counts.pl  1.12  14 years  parrello  *** empty log message ***
compute_new_ids.pl  1.1  15 years  olson  new app for doing updates
compute_pins_and_clusters.pl  1.1  16 years  overbeek  added pins and clusters properly
compute_potential_fusions.pl  1.6  15 years  overbeek  change similarity threshold for computing fusions
compute_sim_chunk.pl  1.1  14 years  olson  Start local sim compuation.
compute_simple_scores.pl  1.3  14 years  overbeek  fixes to computing coupling scores
condense_blast.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
conditionally_assign.pl  1.2  15 years  overbeek  add check to assign_function
connections_between.pl  1.1  14 years  overbeek  connections_between got added
count_bases.pl  1.1  15 years  overbeek  add tree manipulation utilities
das_test.pl  1.1  15 years  olson  das server test script
db_xrefs_of.pl  1.3  14 years  overbeek  fixes to db_xrefs
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...
display_tree.pl  1.3  14 years  redwards  changing displaytree
dna_seq.pl  1.1  15 years  overbeek  interval stuff
exclude_genomes.pl  1.1  15 years  overbeek  Converse of `extract_genomes` --- takes list of genomes to exclude. -- /gdp
expand_blast_table.pl  1.1  16 years  overbeek  remember, .pl
expand_multifunctional_roles.pl  1.2  14 years  overbeek  add make_spreadsheet_and_notes
expand_transferred_chunks.pl  1.3  15 years  overbeek  fix pattern in expand_transferred_chunks
export_genome_as_gff.pl  1.3  14 years  olson  Bundle of misc bob changes, including sim computation code and search-for-substr...
export_similarity_request.pl  1.1  14 years  olson  Script to invoke sim request export.
export_subsystem_as_gff.pl  1.1  14 years  olson  script to write a subsystem as a set of gff files + a spreadsheet.
extend_subsys.pl  1.5  14 years  overbeek  fix error on passing user to index.cgi -- header fix
extend_subsystem.pl  1.1  15 years  olson  add extend_susbsystem script
external_calls.pl  1.1  15 years  overbeek  minor improvements to automated assignments
extract_DNA_for_whole_ORFs.pl  1.1  15 years  overbeek  add start prediction code
extract_DNA_sequence_from_object_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
extract_data_for_syncing_after_update.pl  1.5  15 years  overbeek  package outputs from extract_data_for_syncing_after_update into a directory
extract_data_to_keep.pl  1.4  15 years  overbeek  allow -v on extract_data_to_keep
extract_genes.pl  1.3  14 years  overbeek  add tool to generate gene blocks for variation analysis
extract_genomes.pl  1.25  14 years  overbeek  fixes to extract_genomes
extract_subset_from_sprout_data.pl  1.1  15 years  overbeek  add ability to extract subsets of sprout data
fasta_cksum.c  1.2  15 years  olson  Remove ^Ms
fasta_for_hypo.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
fasta_to_phylip.pl  1.1  15 years  overbeek  lots of data mining stuff
fastasize.c  1.1  14 years  golsen  assess_completeness reads the contigs in one or more specified genome directorie...
fid2dna.pl  1.1  15 years  overbeek  add pegs and fid2dna
fig.pl  1.61.2.1  14 years  olson  Merged from trunk.
fig_net.pl  1.2  15 years  mkubal  script to get ECs with no genes
fig_rpc.pl  1.2  15 years  mkubal  script to get ECs with no genes
fig_specific_sequences.pl  1.1  14 years  overbeek  add fig_specific_sequences
fig_xmlrpc_server.pl  1.4  15 years  mkubal  script to get ECs with no genes
fill_in_cell.pl  1.1  15 years  overbeek  fill_in_cell for Heiko
fill_in_roles.pl  1.3  14 years  overbeek  clean up of auto assignments routines
fill_subsys.pl  1.4  14 years  overbeek  make fill_subsys set user correctly
filter_pegs_in_subsystems.pl  1.3  14 years  overbeek  clean up of auto assignments routines
find_maximal_clusters.pl  1.1  14 years  overbeek  add find_maximal_clusters
fix_eol.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
fix_ext_funcs.pl  1.1  14 years  overbeek  routines to support derivation of sprout data
format_peg_dbs.pl  1.2  14 years  parrello  *** empty log message ***
function_of.pl  1.3  15 years  overbeek  add new subsystem interface
functionally_coupled.pl  1.4  15 years  overbeek  automatically generate aliases from mapped IDs
fusion_of.pl  1.1  15 years  overbeek  add fusion_of
generate_GenomeGroups_for_sprout.pl  1.1  14 years  overbeek  routines to support derivation of sprout data
generate_Property_for_sprout.pl  1.1.2.1  14 years  olson  Merged from trunk.
generate_Source_for_sprout.pl  1.1  14 years  overbeek  routines to support derivation of sprout data
generate_gene_blocks.pl  1.1  14 years  overbeek  add tool to generate gene blocks for variation analysis
generate_genome_feature_tables_for_sprout.pl  1.13  14 years  overbeek  routines to support derivation of sprout data
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...
generate_intergenic_blocks.pl  1.2  14 years  overbeek  fix to generate_intergenic_blocks
generate_kernel_css.pl  1.4  14 years  overbeek  fixes to generate_kernet_css
generate_max_clusters.pl  1.1.2.1  14 years  olson  Merged from trunk.
generate_pin_caches.pl  1.4  14 years  overbeek  fixes to generate_pin_caches
generate_pinned_homologs.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...
generate_sprout_links.pl  1.1  14 years  overbeek  add generate_sprout_links
generate_subsys_tables_for_sprout.pl  1.7  14 years  overbeek  fixes to Sprout Data generation
genome_peg_dna.pl  1.1  14 years  golsen  Tool to dump peg DNA sequences
genomes_of.pl  1.1  15 years  overbeek  basic query tools
get_best_set_of_genes_for_column.pl  1.2  15 years  overbeek  allow set of seeks to cores for bbhs
get_class_examples.pl  1.1  15 years  overbeek  add program to generate class challenge problems
get_dna.pl  1.2  15 years  overbeek  Modified to read from either a file or STDIN. -- /gdp
get_empty_ecs  1.2  15 years  mkubal  6-22 version of get_empty_ecs
get_empty_ecs.pl  1.3  15 years  mkubal  change to EF dir
get_fasta_for_tbl_entries.pl  1.4  15 years  overbeek  Modified to handle included terminal STOP codons. -- /gdp
get_long_enough.pl  1.1  15 years  overbeek  add tree manipulation utilities
get_nr_entries_without_sims.pl  1.2  16 years  overbeek  cleanup issues relating to large numbers of partial genomes
get_pathways_for_EC.pl  1.1  15 years  mkubal  get pathways from KEGG
get_potential_starts_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
get_sims_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
get_translations.pl  1.1  15 years  overbeek  add get_translations
gff2seed.pl  1.5.2.1  14 years  olson  Merged from trunk.
gi2fig.pl  1.2  15 years  overbeek  minor fix to gi2fig
html_parser.py  1.1  15 years  disz  Added html parser for picture making
import_external_sequences_step1.pl  1.7  14 years  overbeek  current external update procedure set
import_external_sequences_step3.pl  1.4  14 years  overbeek  still trying to get the import of external sources right
import_subsystems.pl  1.19  15 years  olson  add commnet
index_annotations.pl  1.5  14 years  parrello  *** empty log message ***
index_contig_files.c  1.2  14 years  olson  Add support for computing MD5 checksums for contigs and genomes. The checksum o...
index_contigs.pl  1.10  14 years  parrello  *** empty log message ***
index_fasta.pl  1.1  15 years  overbeek  add tree manipulation utilities
index_neighborhoods.pl  1.2  14 years  parrello  *** empty log message ***
index_sims.pl  1.8  14 years  parrello  *** empty log message ***
index_sims_file.c  1.1  15 years  olson  Gary Olsen's optimized database loading code. This probably needs to be tweaked...
index_sprout.pl  1.6  14 years  olson  Bundle of misc bob changes, including sim computation code and search-for-substr...
index_subsystems.pl  1.4  14 years  overbeek  use Tracer in index_subsystems
index_translation_files.c  1.1  15 years  olson  Gary Olsen's optimized database loading code. This probably needs to be tweaked...
index_translations.pl  1.14  14 years  olson  Use tac for file reverse on solaris too.
init_FIG.pl  1.6  14 years  parrello  *** empty log message ***
init_dbserver.pl  1.2  15 years  olson  pass requried argument down to call.
init_maps.pl  1.2  14 years  parrello  *** empty log message ***
init_peg_job_scheduler.pl  1.3  14 years  olson  New jobsched stuff.
initial_set.pl  1.1  15 years  overbeek  added two phylogeny tools
insert.pl  1.1  15 years  overbeek  add tree manipulation utilities
insert_all.pl  1.1  15 years  overbeek  add tree manipulation utilities
install-data.pl  1.6  15 years  olson  Fixed up installer.
install_annotations.pl  1.3  15 years  overbeek  attempt to fix package/install for p2p
install_assignments.pl  1.6  15 years  overbeek  sort links
install_code.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
install_feature_updates.pl  1.1  14 years  overbeek  fix by_variant and by_pattern sort codes in subsys.cgi
install_lightweight_code.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
install_subsystems.pl  1.1  15 years  overbeek  p2p changes
install_translation_rules.pl  1.2  16 years  efrank  fixes to p2p
interval.pl  1.1  15 years  overbeek  interval stuff
is_archaeal.pl  1.1  15 years  overbeek  lots of data mining stuff
is_bacterial.pl  1.1  15 years  overbeek  lots of data mining stuff
is_eukaryotic.pl  1.1  15 years  overbeek  lots of data mining stuff
is_prokaryotic.pl  1.1  15 years  overbeek  lots of data mining stuff
keep_only.pl  1.1  14 years  overbeek  add keep_only
lengths_of_contigs.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...
load_attributes.pl  1.14  14 years  parrello  *** empty log message ***
load_bbhs.pl  1.9.2.1  14 years  olson  Merged from trunk.
load_chromosomal_clusters.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
load_close.pl  1.3  14 years  olson  Updated tools for functional coupling computation. Replace string pges with (gen...
load_coupling.pl  1.3.2.1  14 years  olson  Merged from trunk.
load_distances.pl  1.4  14 years  parrello  *** empty log message ***
load_ec_names.pl  1.3  14 years  parrello  *** empty log message ***
load_external_orgs.pl  1.2  14 years  parrello  *** empty log message ***
load_features.pl  1.18  14 years  parrello  *** empty log message ***
load_kegg.pl  1.4  14 years  parrello  *** empty log message ***
load_links.pl  1.5  14 years  overbeek  add make_sprout_upstream
load_literature.pl  1.2  14 years  parrello  *** empty log message ***
load_local_maps.pl  1.2  15 years  olson  Clean up map support.
load_pch_pins.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
load_peg_mapping.pl  1.5  14 years  parrello  *** empty log message ***
load_pirsf.pl  1.6.2.1  14 years  olson  Merged from trunk.
load_protein_families.pl  1.3.2.1  14 years  olson  Merged from trunk.
load_sets.pl  1.4  14 years  parrello  *** empty log message ***
load_sims.pl  1.4  14 years  olson  Updated tools for functional coupling computation. Replace string pges with (gen...
load_sprout.pl  1.25.2.1  14 years  olson  Merged from trunk.
location_of.pl  1.1  14 years  overbeek  filters for data mining
make_PHOBs_for_subsystems.pl  1.4  14 years  overbeek  add tool to generate gene blocks for variation analysis
make_annotations_for_sprout.pl  1.10  14 years  overbeek  additions for sprout
make_assignments_fit_initial_css.pl  1.3  14 years  overbeek  fixes to generation of subsystems from clusters
make_assignments_set.pl  1.2  14 years  overbeek  Ross change commit after cleanup
make_attribute_index.pl  1.2  14 years  mkubal  revised
make_binary.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
make_calls.pl  1.3  14 years  overbeek  cleaned up auto_assign
make_calls_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
make_close.pl  1.1.2.1  14 years  olson  Merged from trunk.
make_close_strain_data.pl  1.4  14 years  overbeek  fix error in usage message for make_close_strain_data
make_indexes.pl  1.9  14 years  parrello  *** empty log message ***
make_maps_from_sub.py  1.4  15 years  olson  test for existence of link before referring to it.
make_match_table.pl  1.1  15 years  overbeek  up max size of bbh extras
make_occ_counts.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
make_phob_from_ids.pl  1.2  14 years  overbeek  Translate selenocystein chars to "X". -- /gdp
make_phob_from_seqs.pl  1.6  14 years  overbeek  fixes to using trees under subsystems
make_protein_sets.pl  1.3  15 years  overbeek  Fixed out-of-mempoy error by replacing backticked grep through NR with pipe-open...
make_rates.pl  1.1  15 years  overbeek  add tree manipulation utilities
make_sim_sets.pl  1.2  16 years  overbeek  fixes from G5 at Fonsteins
make_sim_tab.pl  1.3.2.1  14 years  olson  Merged from trunk.
make_spreadsheet_and_notes.pl  1.2  14 years  overbeek  fixes to generation of subsystems from clusters
make_sprout_upstream.pl  1.1  14 years  overbeek  add make_sprout_upstream
make_subsystems_from_clusters.pl  1.4  14 years  overbeek  fixes to generation of subsystems from clusters
make_transferable_chunks.pl  1.3  15 years  gdpusch  Added error-checking.
make_transferable_tarfiles.pl  1.2  15 years  olson  Make GBrowse work with new Sprout changes.
map_pegs.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
map_sims.pl  1.4  15 years  overbeek  map_sims handles both remapping and deleted
map_sims_for_bigfc.pl  1.1  14 years  olson  Updated tools for functional coupling computation. Replace string pges with (gen...
mark_nr.pl  1.1  15 years  overbeek  up max size of bbh extras
match_dna_to_aligned_prots.pl  1.3  14 years  overbeek  changes to calling starts code
md5.c  1.1  14 years  olson  Add support for computing MD5 checksums for contigs and genomes. The checksum o...
merge_annotations.pl  1.2  14 years  overbeek  additions for sprout
merge_translation_rules.pl  1.6  15 years  overbeek  fix translation rules
order_corrections_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
p2p_daemon.pl  1.1  15 years  olson  standalone daemon for querying for relayed soap requests
p2p_sync_cron.pl  1.2.2.1  14 years  olson  Committing brucella news mods to the news-dev branch.
p2p_sync_from_remote.pl  1.3.2.1  14 years  olson  Committing brucella news mods to the news-dev branch.
package_annotations.pl  1.6  15 years  overbeek  fixes relating to syncing systems during update
package_assignments.pl  1.7  15 years  olson  add usage message
package_code.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...
package_subsystems.pl  1.3  15 years  overbeek  p2p changes
package_translation_rules.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
paint_tree.pl  1.2  15 years  overbeek  generalize paint_tree to handle newick trees
parse_genbank.pl  1.9.2.1  14 years  olson  Merged from trunk.
peg_to_name.pl  1.3  15 years  olson  Some tweaks.
peg_to_pdb.py  1.1  14 years  olson  New script for creating pseudo-pdb files from a peg in the seed.
peg_to_subsystems.pl  1.2  14 years  overbeek  minor updates to peg_to_subsystems
pegs.pl  1.2  15 years  overbeek  interval stuff
pegs_in_conflict.pl  1.2  14 years  overbeek  add clean_subsystems
pegs_in_subsystem.pl  1.4  14 years  overbeek  add pegs_in_conflict
pegs_in_subsystems.pl  1.3  14 years  overbeek  add trim_sequences
possibly_truncated.pl  1.1  14 years  overbeek  add update_subsys_conflicts to fig.pl
postprocess_computed_sims.pl  1.1.2.1  14 years  olson  Merged from trunk.
potentially_cotranscribed.pl  1.1  15 years  overbeek  fixes to aliases_of and added potentially_cotranscribed
pp.pl  1.1  14 years  overbeek  add pp for phylogenetic profiles
predict_starts.pl  1.3  14 years  overbeek  swap clear.corrections and proposed.corrections in calling starts
prep_viz.pl  1.1  15 years  overbeek  add start prediction code
process_new_sims.pl  1.2  14 years  overbeek  Significant changes to syntax and structure. -- /gdp
process_sim_deletions_and_replacements.pl  1.2  14 years  overbeek  various fixes to package/install annotations
project.pl  1.1  14 years  overbeek  add simple tool to investigation of projection
pull_fasta_entries.pl  1.3  14 years  overbeek  add computation of similarities - sims_all and sims_between - between close stra...
pull_orfs.pl  1.2  15 years  overbeek  use FIG in pull_orfs
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...
questionable_calls.pl  1.1  15 years  overbeek  minor improvements to automated assignments
rationalize_blast.pl  1.2  16 years  efrank   fixed a bunch of changes
reduce_sims.pl  1.8  14 years  olson  added some comments
reformat_dsim_dbs.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
reformat_sims.pl  1.2  14 years  overbeek  Made informative msg more informative. -- /gdp
relabel_nodes.pl  1.1  15 years  overbeek  add tree manipulation utilities
relevant_PCHs.pl  1.1  14 years  overbeek  add routines for BigFC
relevant_pchsG.pl  1.2  14 years  olson  Updated tools for functional coupling computation. Replace string pges with (gen...
remove_clustered_pchs.pl  1.4.2.1  14 years  olson  Merged from trunk.
representative_tree.pl  1.1  15 years  overbeek  add tree manipulation utilities
restore_annotations.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...
restore_translation_rules.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
restrict_by_similarity.pl  1.3  15 years  overbeek  fix to restrict_by_similarity
restrict_to_genomes.pl  1.2  15 years  overbeek  more data mining tools
roles_in_subsystem.pl  1.1  14 years  golsen  *** empty log message ***
root_at.pl  1.1  15 years  overbeek  add tree manipulation utilities
run_fc.pl  1.1  14 years  overbeek  add routines for BigFC
run_peg_job_worker.pl  1.3  14 years  olson  New jobsched stuff.
run_start_predictions_for_all_subsystems.pl  1.2  14 years  overbeek  fixes to start predictions
run_start_predictions_for_spreadsheet.pl  1.2  14 years  overbeek  fixes to start predictions
runclustalw.pl  1.2  14 years  overbeek  make runclustalw handle embedded stops
seed2gff.pl  1.2  15 years  redwards  Changes to seed2gff to conform to TIGRs GFF3 suggested output
seed2pir.pl  1.1  14 years  redwards  adding batch command for making seed2pir comparisons
seed_job_scheduler.pl  1.2  15 years  olson  More subsystem/p2p fixes.
select_genomes_for_sprout.pl  1.1  15 years  overbeek  add select_genomes_for_sprout
set_to_relation.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
show_reconfig_cmd.pl  1.2  14 years  olson  add sprout db support.
similar_to.pl  1.3  15 years  overbeek  add error stream for hits as tool runs in similar_to
sims_all.pl  1.1  14 years  overbeek  add computation of similarities - sims_all and sims_between - between close stra...
sims_between.pl  1.1  14 years  overbeek  add computation of similarities - sims_all and sims_between - between close stra...
sort_and_split_bbhs.pl  1.2  14 years  overbeek  Ross change commit after cleanup
split_and_trim_sequences.pl  1.9  14 years  overbeek  fix to split_and_trim
split_sims.pl  1.2  14 years  overbeek  Modified to take input from either STDIN or files; added more informative error-...
splitup.pl  1.3  15 years  gdpusch  Added error-checking.
sprout_search.pl  1.1  15 years  olson  simple cmd interface to sprout search
start_data_for_set_of_pegs.pl  1.1  14 years  overbeek  add tool to generate gene blocks for variation analysis
start_dbserver.pl  1.1  15 years  olson  database server manipulation scripts.
start_services.pl  1.3  15 years  olson  COmmit the service script chagne.
stop_services.pl  1.3  15 years  redwards  Updated stop-services so that it stops the job scheduler
subtree_of.pl  1.1  15 years  overbeek  add subtree_of
sync_new_system.pl  1.4  15 years  overbeek  sort links
tabs2rel.pl  1.1  14 years  overbeek  add tool to generate gene blocks for variation analysis
test_generate_anno_gff.pl  1.2  14 years  olson  Updates to GFF stuff.
test_parse_gff.pl  1.1  14 years  olson  GFF parsing/generation test scripts.
tips_of.pl  1.1  15 years  overbeek  add tree manipulation utilities
to_gids.pl  1.1  15 years  overbeek  utility to convert FIG ids to GI ids
to_insert.pl  1.1  15 years  overbeek  added two phylogeny tools
translate.pl  1.1  15 years  overbeek  add a minimal translation utility
translation_of.pl  1.1  15 years  overbeek  add aliases_of and translation_of filters
trim_sequences.pl  1.5  14 years  overbeek  use neighbor joining, not fitch, to build trees
uninstall.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...
update_sims.pl  1.11  15 years  overbeek  only copy new sim files on update_sims
update_taxonomies.pl  1.6  15 years  overbeek  Converted from "wget" to "curl"
upstream.pl  1.2  15 years  overbeek  lots of data mining stuff
validate_genome_gff.pl  1.4  14 years  olson  fix.
validate_subsystem.pl  1.1  14 years  olson  Basic subsystem package validator. Uses SubsystemFile from P2Pupdate module.
verify_genome_directory.pl  1.18  14 years  overbeek  Added diagnosits for bad STOPs. (Need to add "truncated PEG" logic.) -- /gdp
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...

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