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File Rev. Age Author Last log entry
 Parent Directory        
Makefile  1.13  15 years  golsen  Added fastasize to list of C programs.
README  1.1.1.1  16 years  efrank   import
Simple.pl  1.1  15 years  parrello  *** empty log message ***
add_assertions_of_function.pl  1.20  15 years  overbeek  fixes to extract_genomes
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  1.1  15 years  overbeek  add start prediction code
add_start_data_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
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_with_clustal.pl  1.7  15 years  overbeek  minor fixes to alignments
all_subsystems.pl  1.1  15 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  15 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_hypo.pl  1.2  16 years  overbeek  fixes in auto assignments
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  1.11  15 years  overbeek  fixes to auto_assign
backup_subsystems.pl  1.1  16 years  gdpusch  Script to back up the "Data/Subsystems/" directory. -- /gdp
batch_of_bbhs.pl  1.7  15 years  overbeek  fixes to generation of BBHs
bbhs.pl  1.5  15 years  overbeek  alter length constraint on BBHs
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.
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  15 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  1.1  15 years  overbeek  add start prediction code
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  15 years  overbeek  untested import_external_sequences_step1
build_nr_sources.pl  1.6  15 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  1.4  15 years  overbeek  Fixed bugs and warts in mod to make work as either file or filter. -- /gdp
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...
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  15 years  redwards  changed tag/value pairs completely. Ooops!
compute_changed_ids_for_nrs.pl  1.2  15 years  overbeek  Modified syntax and structure to eliminate mapping step. -- /gdp
compute_genome_counts.pl  1.11  15 years  redwards  addition to gff2seed
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
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
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  15 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  15 years  redwards  changing displaytree
dna_seq.pl  1.1  15 years  overbeek  interval stuff
exclude_genomes.pl  1.1  16 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_transferred_chunks.pl  1.3  16 years  overbeek  fix pattern in expand_transferred_chunks
export_genome_as_gff.pl  1.2  15 years  olson  More export tweaks.
extend_subsys.pl  1.5  15 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  1.2  15 years  overbeek  fixes to start predictions
extract_genomes.pl  1.25  15 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  15 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  1.55  15 years  redwards  many changes to key/value pairs to make them work
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  15 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_subsys.pl  1.4  15 years  overbeek  make fill_subsys set user correctly
fix_eol.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
fix_sprout_annotation_relations.pl  1.1  15 years  overbeek  add fix_sprout_annotation_relations
format_peg_dbs.pl  1.1  15 years  overbeek  fixes to index.cgi to blast against all complete
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_all_bbhs.pl  1.2  15 years  overbeek  minor fix to BBHs
generate_genome_feature_tables_for_sprout.pl  1.11  15 years  overbeek  correct concept of user assign in make_annotations_for_sprout
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_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_subsys_tables_for_sprout.pl  1.6  15 years  overbeek  additions for sprout
genome_peg_dna.pl  1.1  15 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  1.4  15 years  redwards  addition to gff2seed
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  1.4  15 years  overbeek  Fixed to comply with changed `compute_changed_ids_for_nrs` syntax. -- /gdp
import_external_sequences_step3.pl  1.2  15 years  overbeek  Corrected several fatal typos. -- /gdp
import_subsystems.pl  1.19  15 years  olson  add commnet
index_annotations.pl  1.4  16 years  overbeek  add dateof index for annotations
index_contig_files.c  1.2  15 years  olson  Add support for computing MD5 checksums for contigs and genomes. The checksum o...
index_contigs.pl  1.8  15 years  redwards  addition to gff2seed
index_fasta.pl  1.1  15 years  overbeek  add tree manipulation utilities
index_neighborhoods.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
index_sims.pl  1.7  15 years  olson  Doh. Test hte file, not the file number.
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  1.5  15 years  olson  Use $FIG_Config::sproutData instead of FIG_Config::fig/SproutData
index_subsystems.pl  1.2  15 years  overbeek  fix strange situation in indexing 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  1.12  15 years  olson  Remove the debug stmt.
init_FIG.pl  1.5  15 years  olson  modify comment
init_dbserver.pl  1.2  15 years  olson  pass requried argument down to call.
init_maps.pl  1.1  15 years  olson  New map support.
init_peg_job_scheduler.pl  1.3  15 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  16 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  15 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  16 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  15 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  1.9  15 years  redwards  minor changes to marine seed entry and added a new background
load_bbhs.pl  1.5  15 years  overbeek  allow set of seeks to cores for bbhs
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_distances.pl  1.3  15 years  overbeek  minor fix to load_distances
load_ec_names.pl  1.2  16 years  efrank  bobs stuff
load_external_orgs.pl  1.1  16 years  efrank   Makefile: get it to work with the release tools All the rest: had to rename...
load_features.pl  1.17  15 years  overbeek  broaden set of acceptable aliases as dbxrefs
load_kegg.pl  1.3  15 years  overbeek  load_kegg should work now
load_links.pl  1.3  15 years  overbeek  allow 2 or 3 columns in links files
load_literature.pl  1.1  15 years  overbeek  fix bug in subsys.cgi and add Literature to Global
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  1.4  16 years  overbeek  fixed distances and spreadsheet
load_pirsf.pl  1.3  15 years  redwards  changing pir corresepondence
load_protein_families.pl  1.2  16 years  efrank  bobs stuff
load_sets.pl  1.3  15 years  overbeek  minor fixes to exporting sets
load_sprout.pl  1.24  15 years  parrello  *** empty log message ***
location_of.pl  1.1  15 years  overbeek  filters for data mining
make_annotations_for_sprout.pl  1.10  15 years  overbeek  additions for sprout
make_assignments_set.pl  1.1  15 years  overbeek  utility to convert FIG ids to GI ids
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  1.2  15 years  overbeek  Added '-no_hypos' flag to supress function-assignments of "hypotheticals." -- /g...
make_calls_for_start_predictions.pl  1.1  15 years  overbeek  add start prediction code
make_final_condensed_bbhs.pl  1.4  15 years  overbeek  fix bbhs
make_indexes.pl  1.8  15 years  overbeek  fix to make_indexes
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  1.1  15 years  overbeek  pu => phob
make_phob_from_seqs.pl  1.1  15 years  overbeek  pu => phob
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_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
mark_nr.pl  1.1  15 years  overbeek  up max size of bbh extras
match_dna_to_aligned_prots.pl  1.3  15 years  overbeek  changes to calling starts code
md5.c  1.1  15 years  olson  Add support for computing MD5 checksums for contigs and genomes. The checksum o...
merge_annotations.pl  1.2  15 years  overbeek  additions for sprout
merge_translation_rules.pl  1.6  16 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  15 years  olson  fix typos.
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 ...
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  16 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  15 years  gdpusch  Corrected bugs; added checks and debugging information for loci whose sequences ...
peg_to_name.pl  1.3  15 years  olson  Some tweaks.
peg_to_pdb.py  1.1  15 years  olson  New script for creating pseudo-pdb files from a peg in the seed.
peg_to_subsystems.pl  1.2  15 years  overbeek  minor updates to peg_to_subsystems
pegs.pl  1.2  15 years  overbeek  interval stuff
pegs_in_conflict.pl  1.1  15 years  overbeek  add pegs_in_conflict
pegs_in_subsystem.pl  1.4  15 years  overbeek  add pegs_in_conflict
pegs_in_subsystems.pl  1.3  15 years  overbeek  add trim_sequences
possibly_truncated.pl  1.1  15 years  overbeek  add update_subsys_conflicts to fig.pl
potentially_cotranscribed.pl  1.1  15 years  overbeek  fixes to aliases_of and added potentially_cotranscribed
pp.pl  1.1  15 years  overbeek  add pp for phylogenetic profiles
predict_starts.pl  1.3  15 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  15 years  overbeek  Significant changes to syntax and structure. -- /gdp
project.pl  1.1  15 years  overbeek  add simple tool to investigation of projection
pull_fasta_entries.pl  1.2  15 years  overbeek  Modified to ignore whitespace after IDs to pull. -- /gdp
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  15 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  15 years  overbeek  Made informative msg more informative. -- /gdp
relabel_nodes.pl  1.1  15 years  overbeek  add tree manipulation utilities
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  15 years  golsen  *** empty log message ***
root_at.pl  1.1  15 years  overbeek  add tree manipulation utilities
run_peg_job_worker.pl  1.3  15 years  olson  New jobsched stuff.
run_start_predictions_for_all_subsystems.pl  1.2  15 years  overbeek  fixes to start predictions
run_start_predictions_for_spreadsheet.pl  1.2  15 years  overbeek  fixes to start predictions
runclustalw.pl  1.1  15 years  overbeek  add start prediction code
seed2gff.pl  1.2  15 years  redwards  Changes to seed2gff to conform to TIGRs GFF3 suggested output
seed2pir.pl  1.1  15 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  15 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
sort_bbhs_by_counts.pl  1.2  15 years  overbeek  minor error in sort_bbhs_by_counts
split_and_trim_sequences.pl  1.1  14 years  overbeek  fix to show_missing with matches
split_sims.pl  1.2  15 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_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
test_generate_anno_gff.pl  1.2  15 years  olson  Updates to GFF stuff.
test_parse_gff.pl  1.1  15 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  16 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  1.3  15 years  overbeek  add update_subsys_conflicts to fig.pl
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  16 years  overbeek  Converted from "wget" to "curl"
upstream.pl  1.2  15 years  overbeek  lots of data mining stuff
verify_genome_directory.pl  1.17  15 years  overbeek  Added printout of record-number to diagnostic msgs. -- /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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