[Bio] / FigKernelScripts Repository:
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Index of /FigKernelScripts

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File Rev. Age Author (rev) Last log entry
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write_go_mappings.pl (dead) No revisions exist on post-st-migration
where_shifts_occurred.pl (dead) No revisions exist on post-st-migration
where_does_seq_hit.pl (dead) No revisions exist on post-st-migration
weak_predictors.pl (dead) No revisions exist on post-st-migration
wb.pl (dead) No revisions exist on post-st-migration
verify_pegs_in_tbl.pl (dead) No revisions exist on post-st-migration
verify_pegs_in_tbl (dead) No revisions exist on post-st-migration
verify_genome_directory.pl (dead) No revisions exist on post-st-migration
verify_genome_directory (dead) No revisions exist on post-st-migration
validate_subsystem.pl (dead) No revisions exist on post-st-migration
validate_genome_gff.pl (dead) No revisions exist on post-st-migration
validate_fasta.pl (dead) No revisions exist on post-st-migration
valid_fasta_file.pl (dead) No revisions exist on post-st-migration
upstream.pl (dead) No revisions exist on post-st-migration
uproot.pl (dead) No revisions exist on post-st-migration
update_uniq_id_data.pl (dead) No revisions exist on post-st-migration
update_taxonomies.pl (dead) No revisions exist on post-st-migration
update_taxonomies (dead) No revisions exist on post-st-migration
update_sims2.pl (dead) No revisions exist on post-st-migration
update_sims.pl (dead) No revisions exist on post-st-migration
update_sims (dead) No revisions exist on post-st-migration
update_phage_annotations.pl (dead) No revisions exist on post-st-migration
update_nr_cycle.pl (dead) No revisions exist on post-st-migration
update_lineage.pl (dead) No revisions exist on post-st-migration
update_kegg_data.pl (dead) No revisions exist on post-st-migration
update_hope_info.pl (dead) No revisions exist on post-st-migration
update_fr2go.pl (dead) No revisions exist on post-st-migration
update_SSU_rRNAs.pl (dead) No revisions exist on post-st-migration
update_PSEED_subsystems.pl (dead) No revisions exist on post-st-migration
update_OTUs.pl (dead) No revisions exist on post-st-migration
update_FIGfams.pl (dead) No revisions exist on post-st-migration
update-caches.pl (dead) No revisions exist on post-st-migration
uninstall.sims.pl (dead) No revisions exist on post-st-migration
uninstall.sims (dead) No revisions exist on post-st-migration
uninstall.pl (dead) No revisions exist on post-st-migration
uninstall (dead) No revisions exist on post-st-migration
uni_lit_to_dlits.pl (dead) No revisions exist on post-st-migration
trimmed_kernel_alignment.pl (dead) No revisions exist on post-st-migration
trim_sequences.pl (dead) No revisions exist on post-st-migration
trim_alignment.pl (dead) No revisions exist on post-st-migration
translation_of.pl (dead) No revisions exist on post-st-migration
translate_fasta_6.c (dead) No revisions exist on post-st-migration
translate_fasta.c (dead) No revisions exist on post-st-migration
translate.pl (dead) No revisions exist on post-st-migration
trail.pl (dead) No revisions exist on post-st-migration
track_figfams.pl (dead) No revisions exist on post-st-migration
trace.pl (dead) No revisions exist on post-st-migration
tool_hdr_py.pl (dead) No revisions exist on post-st-migration
tool_hdr.pl (dead) No revisions exist on post-st-migration
to_structured_english.pl (dead) No revisions exist on post-st-migration
to_run_new_genomes.sh (dead) No revisions exist on post-st-migration
to_run_daily.sh (dead) No revisions exist on post-st-migration
to_prodom.pl (dead) No revisions exist on post-st-migration
to_org_specific.pl (dead) No revisions exist on post-st-migration
to_map_coords.pl (dead) No revisions exist on post-st-migration
to_insert.pl (dead) No revisions exist on post-st-migration
to_gids.pl (dead) No revisions exist on post-st-migration
to_gg.pl (dead) No revisions exist on post-st-migration
to_genbank.pl (dead) No revisions exist on post-st-migration
to_fasta.pl (dead) No revisions exist on post-st-migration
to_arabidopsis.pl (dead) No revisions exist on post-st-migration
tmpred_predictions.pl (dead) No revisions exist on post-st-migration
tips_of.pl (dead) No revisions exist on post-st-migration
test_placement.pl (dead) No revisions exist on post-st-migration
test_parse_gff.pl (dead) No revisions exist on post-st-migration
test_generate_anno_gff.pl (dead) No revisions exist on post-st-migration
test_figfam_placement_into_families.pl (dead) No revisions exist on post-st-migration
test_figfam_peg.pl (dead) No revisions exist on post-st-migration
test_figfam_FF_peg.pl (dead) No revisions exist on post-st-migration
test_cv.pl (dead) No revisions exist on post-st-migration
test_cv.expected (dead) No revisions exist on post-st-migration
test_Observation.pl (dead) No revisions exist on post-st-migration
tbl_to_gto.pl (dead) No revisions exist on post-st-migration
tabs2rel.pl (dead) No revisions exist on post-st-migration
synchronize_annotations_and_assignments.pl (dead) No revisions exist on post-st-migration
sync_new_system.pl (dead) No revisions exist on post-st-migration
svr_with_close_blast_hits.pl (dead) No revisions exist on post-st-migration
svr_which_genus_species.pl (dead) No revisions exist on post-st-migration
svr_upstream.pl (dead) No revisions exist on post-st-migration
svr_update_corr_maps.pl (dead) No revisions exist on post-st-migration
svr_update_assignments.pl (dead) No revisions exist on post-st-migration
svr_trim_ali.pl (dead) No revisions exist on post-st-migration
svr_tree_to_html.pl (dead) No revisions exist on post-st-migration
svr_tree.pl (dead) No revisions exist on post-st-migration
svr_translations_of.pl (dead) No revisions exist on post-st-migration
svr_tmpred_predictions.pl (dead) No revisions exist on post-st-migration
svr_tips_of_tree.pl (dead) No revisions exist on post-st-migration
svr_taxonomy.pl (dead) No revisions exist on post-st-migration
svr_taxonomically_related_genomes.pl (dead) No revisions exist on post-st-migration
svr_tab2html.pl (dead) No revisions exist on post-st-migration
svr_summarize_protein_families.pl (dead) No revisions exist on post-st-migration
svr_summarize_contigs.pl (dead) No revisions exist on post-st-migration
svr_summarize_MG_output.pl (dead) No revisions exist on post-st-migration
svr_subsystems_to_roles.pl (dead) No revisions exist on post-st-migration
svr_subsystem_spreadsheet.pl (dead) No revisions exist on post-st-migration
svr_subsystem_roles.pl (dead) No revisions exist on post-st-migration
svr_subsystem_genomes.pl (dead) No revisions exist on post-st-migration
svr_subsystem_genome_data.pl (dead) No revisions exist on post-st-migration
svr_subsystem_classification.pl (dead) No revisions exist on post-st-migration
svr_submit_correspondences.pl (dead) No revisions exist on post-st-migration
svr_submit_RAST_job.pl (dead) No revisions exist on post-st-migration
svr_status_of_RAST_job.pl (dead) No revisions exist on post-st-migration
svr_ss_classes.pl (dead) No revisions exist on post-st-migration
svr_spreadsheet_to_file.pl (dead) No revisions exist on post-st-migration
svr_split_fams.pl (dead) No revisions exist on post-st-migration
svr_sphinx_indexing.pl (dead) No revisions exist on post-st-migration
svr_sketch_tree.pl (dead) No revisions exist on post-st-migration
svr_sims2html.pl (dead) No revisions exist on post-st-migration
svr_similar_to.pl (dead) No revisions exist on post-st-migration
svr_sets_by_owner.pl (dead) No revisions exist on post-st-migration
svr_seed_to_table.pl (dead) No revisions exist on post-st-migration
svr_seed_to_genbank.pl (dead) No revisions exist on post-st-migration
svr_seed_to_embl.pl (dead) No revisions exist on post-st-migration
svr_scripts.t (dead) No revisions exist on post-st-migration
svr_scanP.pl (dead) No revisions exist on post-st-migration
svr_scanN.pl (dead) No revisions exist on post-st-migration
svr_run_rast_jobs.pl (dead) No revisions exist on post-st-migration
svr_run_RAST_jobs.pl (dead) No revisions exist on post-st-migration
svr_roles_to_subsys.pl (dead) No revisions exist on post-st-migration
svr_roles_to_reactions.pl (dead) No revisions exist on post-st-migration
svr_role_to_pegs.pl (dead) No revisions exist on post-st-migration
svr_role_to_complex.pl (dead) No revisions exist on post-st-migration
svr_retrieve_RAST_job.pl (dead) No revisions exist on post-st-migration
svr_reroot_tree.pl (dead) No revisions exist on post-st-migration
svr_representative_sequences.pl (dead) No revisions exist on post-st-migration
svr_rep_seqs.pl (dead) No revisions exist on post-st-migration
svr_regulons_to_fids.pl (dead) No revisions exist on post-st-migration
svr_reactions_to_roles.pl (dead) No revisions exist on post-st-migration
svr_reactions_in_model.pl (dead) No revisions exist on post-st-migration
svr_reaction_gain_loss_table.pl (dead) No revisions exist on post-st-migration
svr_reaction_description.pl (dead) No revisions exist on post-st-migration
svr_rRNA.pl (dead) No revisions exist on post-st-migration
svr_quick_assign.pl (dead) No revisions exist on post-st-migration
svr_put_set.pl (dead) No revisions exist on post-st-migration
svr_psiblast_search.pl (dead) No revisions exist on post-st-migration
svr_protein_assertions.pl (dead) No revisions exist on post-st-migration
svr_project_model.pl (dead) No revisions exist on post-st-migration
svr_project_by_sr.pl (dead) No revisions exist on post-st-migration
svr_preferred_roles.pl (dead) No revisions exist on post-st-migration
svr_possible_joins.pl (dead) No revisions exist on post-st-migration
svr_pegs_with_evcode.pl (dead) No revisions exist on post-st-migration
svr_pegs_in_subsystems.pl (dead) No revisions exist on post-st-migration
svr_otus.pl (dead) No revisions exist on post-st-migration
svr_oligomer_similarity.pl (dead) No revisions exist on post-st-migration
svr_neighbors_of.pl (dead) No revisions exist on post-st-migration
svr_neighboring_reactions.pl (dead) No revisions exist on post-st-migration
svr_neighborhood_of_role.pl (dead) No revisions exist on post-st-migration
svr_motif.pl (dead) No revisions exist on post-st-migration
svr_missing_roles.pl (dead) No revisions exist on post-st-migration
svr_metabolic_reconstruction.pl (dead) No revisions exist on post-st-migration
svr_members_of_otu.pl (dead) No revisions exist on post-st-migration
svr_md5_of_prot.pl (dead) No revisions exist on post-st-migration
svr_mark_tree_states.pl (dead) No revisions exist on post-st-migration
svr_mapped_genomes.pl (dead) No revisions exist on post-st-migration
svr_make_pan_genome_prot_families.pl (dead) No revisions exist on post-st-migration
svr_location_of.pl (dead) No revisions exist on post-st-migration
svr_link_to_compare_regions.pl (dead) No revisions exist on post-st-migration
svr_kill_RAST_job.pl (dead) No revisions exist on post-st-migration
svr_keep_only.pl (dead) No revisions exist on post-st-migration
svr_just_ends.pl (dead) No revisions exist on post-st-migration
svr_is_hypo.pl (dead) No revisions exist on post-st-migration
svr_intergenic_regions.pl (dead) No revisions exist on post-st-migration
svr_insert_seqs_into_alignment.pl (dead) No revisions exist on post-st-migration
svr_inherit_annotations.pl (dead) No revisions exist on post-st-migration
svr_inherit_aliases.pl (dead) No revisions exist on post-st-migration
svr_inconsistent_sets.pl (dead) No revisions exist on post-st-migration
svr_in_runs.pl (dead) No revisions exist on post-st-migration
svr_in_fasta.pl (dead) No revisions exist on post-st-migration
svr_img_analysis.pl (dead) No revisions exist on post-st-migration
svr_ids_to_subsystems.pl (dead) No revisions exist on post-st-migration
svr_ids_to_figfams.pl (dead) No revisions exist on post-st-migration
svr_identical_genomes.pl (dead) No revisions exist on post-st-migration
svr_get_set.pl (dead) No revisions exist on post-st-migration
svr_get_rep_genomes.pl (dead) No revisions exist on post-st-migration
svr_get_default_dataset.pl (dead) No revisions exist on post-st-migration
svr_get_coupling_data.pl (dead) No revisions exist on post-st-migration
svr_get_all.pl (dead) No revisions exist on post-st-migration
svr_get_ali_and_tree.pl (dead) No revisions exist on post-st-migration
svr_genome_statistics.pl (dead) No revisions exist on post-st-migration
svr_genome_of.pl (dead) No revisions exist on post-st-migration
svr_genome_functions.pl (dead) No revisions exist on post-st-migration
svr_generate_dna_samples.pl (dead) No revisions exist on post-st-migration
svr_gene_data.pl (dead) No revisions exist on post-st-migration
svr_genbank_to_table.pl (dead) No revisions exist on post-st-migration
svr_genbank_to_seed.pl (dead) No revisions exist on post-st-migration
svr_gap_filled_reactions_and_roles.pl (dead) No revisions exist on post-st-migration
svr_functionally_coupled.pl (dead) No revisions exist on post-st-migration
svr_function_to_role.pl (dead) No revisions exist on post-st-migration
svr_function_of.pl (dead) No revisions exist on post-st-migration
svr_find_regulatory_proteins.pl (dead) No revisions exist on post-st-migration
svr_find_protein.pl (dead) No revisions exist on post-st-migration
svr_find_hypos_for_cluster.pl (dead) No revisions exist on post-st-migration
svr_find_fused_genes.pl (dead) No revisions exist on post-st-migration
svr_find_clusters_relevant_to_role.pl (dead) No revisions exist on post-st-migration
svr_find_clusters_relevant_to_reaction.pl (dead) No revisions exist on post-st-migration
svr_file_to_spreadsheet.pl (dead) No revisions exist on post-st-migration
svr_figfams_to_ids.pl (dead) No revisions exist on post-st-migration
svr_figfam_functions.pl (dead) No revisions exist on post-st-migration
svr_figfam_fasta.pl (dead) No revisions exist on post-st-migration
svr_fig_id_corr.pl (dead) No revisions exist on post-st-migration
svr_fids_to_regulons.pl (dead) No revisions exist on post-st-migration
svr_fids_to_locations.pl (dead) No revisions exist on post-st-migration
svr_fids_to_ids.pl (dead) No revisions exist on post-st-migration
svr_fids_for_md5.pl (dead) No revisions exist on post-st-migration
svr_fc_figfams.pl (dead) No revisions exist on post-st-migration
svr_fasta_to_md5.pl (dead) No revisions exist on post-st-migration
svr_fasta.pl (dead) No revisions exist on post-st-migration
svr_expressed_genes_in_range.pl (dead) No revisions exist on post-st-migration
svr_export_as_seed_dir.pl (dead) No revisions exist on post-st-migration
svr_exp_genomes.pl (dead) No revisions exist on post-st-migration
svr_evidence.pl (dead) No revisions exist on post-st-migration
svr_enumerate_sets_by_owner.pl (dead) No revisions exist on post-st-migration
svr_drug_resistance_proteins.pl (dead) No revisions exist on post-st-migration
svr_dna_seq.pl (dead) No revisions exist on post-st-migration
svr_dlits.pl (dead) No revisions exist on post-st-migration
svr_distinct_otus.pl (dead) No revisions exist on post-st-migration
svr_discriminating_functions.pl (dead) No revisions exist on post-st-migration
svr_determine_sets_of_related_contigs.pl (dead) No revisions exist on post-st-migration
svr_delete_set.pl (dead) No revisions exist on post-st-migration
svr_delete_from_set.pl (dead) No revisions exist on post-st-migration
svr_delete_RAST_job.pl (dead) No revisions exist on post-st-migration
svr_cut_domain.pl (dead) No revisions exist on post-st-migration
svr_current_annotation.pl (dead) No revisions exist on post-st-migration
svr_create_set.pl (dead) No revisions exist on post-st-migration
svr_coupled_reactions.pl (dead) No revisions exist on post-st-migration
svr_corresponding_genes2.pl (dead) No revisions exist on post-st-migration
svr_corresponding_genes.pl (dead) No revisions exist on post-st-migration
svr_corr_by_exp.pl (dead) No revisions exist on post-st-migration
svr_coregulated_by_correspondence.pl (dead) No revisions exist on post-st-migration
svr_copy_to_RAST_dir.pl (dead) No revisions exist on post-st-migration
svr_contigs_in_genome.pl (dead) No revisions exist on post-st-migration
svr_condense_repeats.pl (dead) No revisions exist on post-st-migration
svr_complex_to_reaction.pl (dead) No revisions exist on post-st-migration
svr_compare_feature_tables.pl (dead) No revisions exist on post-st-migration
svr_column_of_subsystem.pl (dead) No revisions exist on post-st-migration
svr_cohesion_groups.pl (dead) No revisions exist on post-st-migration
svr_co_occurrence_evidence.pl (dead) No revisions exist on post-st-migration
svr_co_occurrence.pl (dead) No revisions exist on post-st-migration
svr_cluster_pegs.pl (dead) No revisions exist on post-st-migration
svr_cluster_locations.pl (dead) No revisions exist on post-st-migration
svr_closest_genes.pl (dead) No revisions exist on post-st-migration
svr_close_genomes.pl (dead) No revisions exist on post-st-migration
svr_cdd_scan.pl (dead) No revisions exist on post-st-migration
svr_call_rnas.pl (dead) No revisions exist on post-st-migration
svr_call_pegs.pl (dead) No revisions exist on post-st-migration
svr_by_taxonomy.pl (dead) No revisions exist on post-st-migration
svr_blast.pl (dead) No revisions exist on post-st-migration
svr_big_repeats.pl (dead) No revisions exist on post-st-migration
svr_atomic_regulons.pl (dead) No revisions exist on post-st-migration
svr_atomic_reg_coexp.pl (dead) No revisions exist on post-st-migration
svr_assign_using_figfams.pl (dead) No revisions exist on post-st-migration
svr_assign_to_dna_using_figfams.pl (dead) No revisions exist on post-st-migration
svr_all_subsystems.pl (dead) No revisions exist on post-st-migration
svr_all_roles_used_in_models.pl (dead) No revisions exist on post-st-migration
svr_all_reactions.pl (dead) No revisions exist on post-st-migration
svr_all_models.pl (dead) No revisions exist on post-st-migration
svr_all_genomes.pl (dead) No revisions exist on post-st-migration
svr_all_figfams.pl (dead) No revisions exist on post-st-migration
svr_all_features.pl (dead) No revisions exist on post-st-migration
svr_all_experiments.pl (dead) No revisions exist on post-st-migration
svr_all_complexes.pl (dead) No revisions exist on post-st-migration
svr_aligns_with_prot.pl (dead) No revisions exist on post-st-migration
svr_align_using_muscle.pl (dead) No revisions exist on post-st-migration
svr_align_seqs.pl (dead) No revisions exist on post-st-migration
svr_aliases_to_pegs.pl (dead) No revisions exist on post-st-migration
svr_aliases_of.pl (dead) No revisions exist on post-st-migration
svr_ali_to_html.pl (dead) No revisions exist on post-st-migration
svr_add_reaction_descriptions.pl (dead) No revisions exist on post-st-migration
svr_add_lengths_to_blast.pl (dead) No revisions exist on post-st-migration
svr_ach_lookup.pl (dead) No revisions exist on post-st-migration
svr_SAP.t (dead) No revisions exist on post-st-migration
svr_RNA_genes.pl (dead) No revisions exist on post-st-migration
svr_NCBI_taxonomy.pl (dead) No revisions exist on post-st-migration
svr_NCBI_sequence.pl (dead) No revisions exist on post-st-migration
svr_CS_pipeline.pl (dead) No revisions exist on post-st-migration
svr_CS.pl (dead) No revisions exist on post-st-migration
svr_ACH.t (dead) No revisions exist on post-st-migration
svr.pl (dead) No revisions exist on post-st-migration
svc_fasta_to_md5.pl (dead) No revisions exist on post-st-migration
summarize_taxonomy_by_blast.pl (dead) No revisions exist on post-st-migration
summarize_genome_data.pl (dead) No revisions exist on post-st-migration
summarize_classification_data.pl (dead) No revisions exist on post-st-migration
subtree_of.pl (dead) No revisions exist on post-st-migration
subsys_info.pl (dead) No revisions exist on post-st-migration
subsys2pubmed.pl (dead) No revisions exist on post-st-migration
submit_to_iprscan_on_biocluster.pl (dead) No revisions exist on post-st-migration
submit_genome_to_signalP.pl (dead) No revisions exist on post-st-migration
submit_genome_to_rpsblast_against_CDD_on_biocluster.pl (dead) No revisions exist on post-st-migration
submit_ff_test.pl (dead) No revisions exist on post-st-migration
submit_corr_to_server.pl (dead) No revisions exist on post-st-migration
submit_corr.pl (dead) No revisions exist on post-st-migration
stop_services.pl (dead) No revisions exist on post-st-migration
start_services.pl (dead) No revisions exist on post-st-migration
start_dbserver.pl (dead) No revisions exist on post-st-migration
start_data_for_set_of_pegs.pl (dead) No revisions exist on post-st-migration
sr_pipeline.pl (dead) No revisions exist on post-st-migration
sprout_search.pl (dead) No revisions exist on post-st-migration
splitup.pl (dead) No revisions exist on post-st-migration
splitup (dead) No revisions exist on post-st-migration
split_sims.pl (dead) No revisions exist on post-st-migration
split_sequences_into_sets.pl (dead) No revisions exist on post-st-migration
split_fasta.pl (dead) No revisions exist on post-st-migration
split_clean_unclean_families.pl (dead) No revisions exist on post-st-migration
split_by_genome.pl (dead) No revisions exist on post-st-migration
split_assignments_based_on_subsystems.pl (dead) No revisions exist on post-st-migration
split_and_trim_sequences.pl (dead) No revisions exist on post-st-migration
split_and_install_pchs.pl (dead) No revisions exist on post-st-migration
sphinx_index_genome.pl (dead) No revisions exist on post-st-migration
sparse_genome_sample.pl (dead) No revisions exist on post-st-migration
sp2fasta.pl (dead) No revisions exist on post-st-migration
sort_sets_of_pegs.pl (dead) No revisions exist on post-st-migration
sort_by_function.pl (dead) No revisions exist on post-st-migration
sort_by_annotator.pl (dead) No revisions exist on post-st-migration
sort_bbhs_by_counts.pl (dead) No revisions exist on post-st-migration
sort_and_split_bbhs.pl (dead) No revisions exist on post-st-migration
solid_rectangles_to_solid_families.pl (dead) No revisions exist on post-st-migration
sketch_tree.pl (dead) No revisions exist on post-st-migration
sims_between.pl (dead) No revisions exist on post-st-migration
sims_all.pl (dead) No revisions exist on post-st-migration
sims_after_adding_genome.pl (dead) No revisions exist on post-st-migration
similar_to.pl (dead) No revisions exist on post-st-migration
sigs.pl (dead) No revisions exist on post-st-migration
show_structured_english.pl (dead) No revisions exist on post-st-migration
show_reconfig_cmd.pl (dead) No revisions exist on post-st-migration
set_to_relation.pl (dead) No revisions exist on post-st-migration
set_to_relation (dead) No revisions exist on post-st-migration
set_not_private.pl (dead) No revisions exist on post-st-migration
set_figfam_functions.pl (dead) No revisions exist on post-st-migration
set_by_subtree.pl (dead) No revisions exist on post-st-migration
set-from-subtree.pl (dead) No revisions exist on post-st-migration
server_paper_figure2.pl (dead) No revisions exist on post-st-migration
server_paper_example7.pl (dead) No revisions exist on post-st-migration
server_paper_example6.pl (dead) No revisions exist on post-st-migration
server_paper_example5.pl (dead) No revisions exist on post-st-migration
server_paper_example4.pl (dead) No revisions exist on post-st-migration
server_paper_example3.pl (dead) No revisions exist on post-st-migration
server_paper_example2.pl (dead) No revisions exist on post-st-migration
server_paper_example1b.pl (dead) No revisions exist on post-st-migration
server_paper_example1a.pl (dead) No revisions exist on post-st-migration
server_paper_example1.pl (dead) No revisions exist on post-st-migration
sequence_length_histogram.pl (dead) No revisions exist on post-st-migration
sequence_dereplication.pl (dead) No revisions exist on post-st-migration
select_genomes_for_sprout.pl (dead) No revisions exist on post-st-migration
seed_run_task.pl (dead) No revisions exist on post-st-migration
seed_run_job.pl (dead) No revisions exist on post-st-migration
seed_job_scheduler.pl (dead) No revisions exist on post-st-migration
seed2txt.pl (dead) No revisions exist on post-st-migration
seed2tbl.pl (dead) No revisions exist on post-st-migration
seed2ptt.pl (dead) No revisions exist on post-st-migration
seed2pir.pl (dead) No revisions exist on post-st-migration
seed2gff.pl (dead) No revisions exist on post-st-migration
seed2genbank.pl (dead) No revisions exist on post-st-migration
score_ifcs_mcauliffe.pl (dead) No revisions exist on post-st-migration
score_ifcs.pl (dead) No revisions exist on post-st-migration
score_dfcs_mcauliffe.pl (dead) No revisions exist on post-st-migration
score_dfcs.pl (dead) No revisions exist on post-st-migration
same_subsys.pl (dead) No revisions exist on post-st-migration
same_figfam.pl (dead) No revisions exist on post-st-migration
salvage_subsystem_rows.pl (dead) No revisions exist on post-st-migration
salvage_on_replacement.pl (dead) No revisions exist on post-st-migration
salvage_master_annotations.pl (dead) No revisions exist on post-st-migration
salvage_annotations.pl (dead) No revisions exist on post-st-migration
runclustalw.pl (dead) No revisions exist on post-st-migration
run_start_predictions_for_spreadsheet.pl (dead) No revisions exist on post-st-migration
run_start_predictions_for_all_subsystems.pl (dead) No revisions exist on post-st-migration
run_scenarios.pl (dead) No revisions exist on post-st-migration
run_ribo_ratio_against_pubseed.pl (dead) No revisions exist on post-st-migration
run_remote_Phobius_for_genomes.pl (dead) No revisions exist on post-st-migration
run_remote_Phobius_for_genome_for_RAST.pl (dead) No revisions exist on post-st-migration
run_remote_Phobius_for_genome.pl (dead) No revisions exist on post-st-migration
run_remote_Phobius_for_fasta.pl (dead) No revisions exist on post-st-migration
run_remote_PHOBIOUS.pl (dead) No revisions exist on post-st-migration
run_rabbit_daemon_set.pl (dead) No revisions exist on post-st-migration
run_rabbit_daemon.pl (dead) No revisions exist on post-st-migration
run_peg_job_worker.pl (dead) No revisions exist on post-st-migration
run_muscle.pl (dead) No revisions exist on post-st-migration
run_model_generation_v3.pl (dead) No revisions exist on post-st-migration
run_model_generation_all.pl (dead) No revisions exist on post-st-migration
run_model_generation.pl (dead) No revisions exist on post-st-migration
run_glimmer3.pl (dead) No revisions exist on post-st-migration
run_glimmer2.pl (dead) No revisions exist on post-st-migration
run_gene_calling_scripts.pl (dead) No revisions exist on post-st-migration
run_flux_optimization.pl (dead) No revisions exist on post-st-migration
run_find_subsys_against_all_genomes.pl (dead) No revisions exist on post-st-migration
run_fc.pl (dead) No revisions exist on post-st-migration
run_coreseed_to_pubseed_flow.sh (dead) No revisions exist on post-st-migration
run_checkm.pl (dead) No revisions exist on post-st-migration
run_anno_to_pubseed_flow.sh (dead) No revisions exist on post-st-migration
run_all_inference.pl (dead) No revisions exist on post-st-migration
run_all_fam_rel.pl (dead) No revisions exist on post-st-migration
run_HMM_search_on_timelogic.pl (dead) No revisions exist on post-st-migration
run1_convergence_step.pl (dead) No revisions exist on post-st-migration
rs_pipeline.pl (dead) No revisions exist on post-st-migration
rs_get_rnas.pl (dead) No revisions exist on post-st-migration
rs_get_peg_counts.pl (dead) No revisions exist on post-st-migration
rs_get_intergenic_counts.pl (dead) No revisions exist on post-st-migration
rs_create_ref_profile.pl (dead) No revisions exist on post-st-migration
rs.pl (dead) No revisions exist on post-st-migration
root_at_midpoint.pl (dead) No revisions exist on post-st-migration
root_at.pl (dead) No revisions exist on post-st-migration
roles_in_subsystem.pl (dead) No revisions exist on post-st-migration
rewrite_peg_syns.pl (dead) No revisions exist on post-st-migration
restrict_to_genomes.pl (dead) No revisions exist on post-st-migration
restrict_by_similarity.pl (dead) No revisions exist on post-st-migration
restore_translation_rules.pl (dead) No revisions exist on post-st-migration
restore_translation_rules (dead) No revisions exist on post-st-migration
restore_assignments.pl (dead) No revisions exist on post-st-migration
restore_assignments (dead) No revisions exist on post-st-migration
restore_annotations.pl (dead) No revisions exist on post-st-migration
restore_annotations (dead) No revisions exist on post-st-migration
reps_for_wc.pl (dead) No revisions exist on post-st-migration
reps_and_close.pl (dead) No revisions exist on post-st-migration
representative_tree.pl (dead) No revisions exist on post-st-migration
representative_sequences.pl (dead) No revisions exist on post-st-migration
report_changes.pl (dead) No revisions exist on post-st-migration
rep_sets.pl (dead) No revisions exist on post-st-migration
rep_genomes.pl (dead) No revisions exist on post-st-migration
renumber_seed_dir.pl (dead) No revisions exist on post-st-migration
renumber_features.pl (dead) No revisions exist on post-st-migration
remove_sims_not_in_nr.pl (dead) No revisions exist on post-st-migration
remove_rna_overlaps.pl (dead) No revisions exist on post-st-migration
remove_multiple_occurring_probes.pl (dead) No revisions exist on post-st-migration
remove_embedded_pegs.pl (dead) No revisions exist on post-st-migration
remove_clustered_pchs3.pl (dead) No revisions exist on post-st-migration
remove_clustered_pchs2.pl (dead) No revisions exist on post-st-migration
remove_clustered_pchs.pl (dead) No revisions exist on post-st-migration
relevant_pchsG.pl (dead) No revisions exist on post-st-migration
relevant_PCHs.pl (dead) No revisions exist on post-st-migration
relabel_nodes.pl (dead) No revisions exist on post-st-migration
rel2tabs.pl (dead) No revisions exist on post-st-migration
reindex_sim_btrees.pl (dead) No revisions exist on post-st-migration
register_genome_with_clearinghouse.pl (dead) No revisions exist on post-st-migration
register_features_with_clearinghouse.pl (dead) No revisions exist on post-st-migration
register_features_batch.pl (dead) No revisions exist on post-st-migration
reformat_timelogic_sims.pl (dead) No revisions exist on post-st-migration
reformat_sims.pl (dead) No revisions exist on post-st-migration
reformat_sims (dead) No revisions exist on post-st-migration
reformat_fasta.pl (dead) No revisions exist on post-st-migration
reformat_dsim_dbs.pl (dead) No revisions exist on post-st-migration
reformat_dsim_dbs (dead) No revisions exist on post-st-migration
reformat_contigs.pl (dead) No revisions exist on post-st-migration
reformat_circular_contigs.pl (dead) No revisions exist on post-st-migration
reduce_sims.pl (dead) No revisions exist on post-st-migration
reduce_sims (dead) No revisions exist on post-st-migration
recompute_comparison.pl (dead) No revisions exist on post-st-migration
recent_annotations_by_genome.pl (dead) No revisions exist on post-st-migration
recall_pegs.pl (dead) No revisions exist on post-st-migration
rebuild_global_chromosomal_clusters.pl (dead) No revisions exist on post-st-migration
rebuild_converged_Data.pl (dead) No revisions exist on post-st-migration
readable_fasta.pl (dead) No revisions exist on post-st-migration
read_write_excel.pl (dead) No revisions exist on post-st-migration
rationalize_blast.pl (dead) No revisions exist on post-st-migration
rationalize_blast (dead) No revisions exist on post-st-migration
rast_prepare_NR_directory.pl (dead) No revisions exist on post-st-migration
rast_load_specialty_genes.pl (dead) No revisions exist on post-st-migration
rast_export_genome.pl (dead) No revisions exist on post-st-migration
rast_delete_rejected_pegs.pl (dead) No revisions exist on post-st-migration
rast_compute_specialty_genes.pl (dead) No revisions exist on post-st-migration
rast_call_tRNAs.pl (dead) No revisions exist on post-st-migration
rast_call_special_proteins.pl (dead) No revisions exist on post-st-migration
rast_call_rRNAs.pl (dead) No revisions exist on post-st-migration
rast_call_prophage_using_phispy.pl (dead) No revisions exist on post-st-migration
rast_call_crisprs.pl (dead) No revisions exist on post-st-migration
rast_call_assembly_gaps.pl (dead) No revisions exist on post-st-migration
rast_call_RNAs.pl (dead) No revisions exist on post-st-migration
rast_call_CDSs_using_prodigal.pl (dead) No revisions exist on post-st-migration
rast_build_nr_from_close_genomes.pl (dead) No revisions exist on post-st-migration
rast_annotate_proteins_similarity.pl (dead) No revisions exist on post-st-migration
rapid_subsystem_inference_batch.pl (dead) No revisions exist on post-st-migration
rapid_subsystem_inference.pl (dead) No revisions exist on post-st-migration
rapid_propagation_plasmid.pl (dead) No revisions exist on post-st-migration
rapid_propagation5.pl (dead) No revisions exist on post-st-migration
rapid_propagation4.pl (dead) No revisions exist on post-st-migration
rapid_propagation3.pl (dead) No revisions exist on post-st-migration
rapid_propagation2.pl (dead) No revisions exist on post-st-migration
rapid_propagation.pl (dead) No revisions exist on post-st-migration
questionable_calls.pl (dead) No revisions exist on post-st-migration
put_func_on_families_2c.pl (dead) No revisions exist on post-st-migration
put_directory_in_one_file.pl (dead) No revisions exist on post-st-migration
put_directory_in_one_file (dead) No revisions exist on post-st-migration
purge_tbl.pl (dead) No revisions exist on post-st-migration
purge_fasta.pl (dead) No revisions exist on post-st-migration
pull_sp_entries.pl (dead) No revisions exist on post-st-migration
pull_orfs.pl (dead) No revisions exist on post-st-migration
pull_fasta_entries.pl (dead) No revisions exist on post-st-migration
pull_fasta_entries (dead) No revisions exist on post-st-migration
pubseed_data_export.pl (dead) No revisions exist on post-st-migration
pubmed_gene2peg.pl (dead) No revisions exist on post-st-migration
publish_subsystems.pl (dead) No revisions exist on post-st-migration
pubbed_fids.pl (dead) No revisions exist on post-st-migration
propagate_subsys_changes_to_figfams.pl (dead) No revisions exist on post-st-migration
promote_orfs_to_pegs.pl (dead) No revisions exist on post-st-migration
project_codon_usage_onto_axis.c (dead) No revisions exist on post-st-migration
project.pl (dead) No revisions exist on post-st-migration
process_sim_deletions_and_replacements.pl (dead) No revisions exist on post-st-migration
process_otus.pl (dead) No revisions exist on post-st-migration
process_one_exp_dir.pl (dead) No revisions exist on post-st-migration
process_new_sims.pl (dead) No revisions exist on post-st-migration
process_new_sims (dead) No revisions exist on post-st-migration
process_genomes.pl (dead) No revisions exist on post-st-migration
process_evaluation.pl (dead) No revisions exist on post-st-migration
prepare_metagenome_files_for_ftp.pl (dead) No revisions exist on post-st-migration
prepare_metagenome_files_for_download.pl (dead) No revisions exist on post-st-migration
prep_viz.pl (dead) No revisions exist on post-st-migration
predicted_vs_actual.pl (dead) No revisions exist on post-st-migration
predict_starts.pl (dead) No revisions exist on post-st-migration
predict_scenarios.pl (dead) No revisions exist on post-st-migration
pp.pl (dead) No revisions exist on post-st-migration
potentially_missed_assignments.pl (dead) No revisions exist on post-st-migration
potentially_cotranscribed.pl (dead) No revisions exist on post-st-migration
postprocess_computed_sims.pl (dead) No revisions exist on post-st-migration
possibly_truncated.pl (dead) No revisions exist on post-st-migration
possible_projections.pl (dead) No revisions exist on post-st-migration
possible_frameshifts.pl (dead) No revisions exist on post-st-migration
pop_vec.pl (dead) No revisions exist on post-st-migration
plate_sheet_parser.pl (dead) No revisions exist on post-st-migration
place_proteins_into_pattyfams.pl (dead) No revisions exist on post-st-migration
place_properties_on_tree.pl (dead) No revisions exist on post-st-migration
pick_feature_set.pl (dead) No revisions exist on post-st-migration
pg_tabulate_reactions.pl (dead) No revisions exist on post-st-migration
pg_submit_to_RAST.pl (dead) No revisions exist on post-st-migration
pg_run_gapfills.pl (dead) No revisions exist on post-st-migration
pg_roles_in_some_but_not_X.pl (dead) No revisions exist on post-st-migration
pg_process_pubs.pl (dead) No revisions exist on post-st-migration
pg_pipeline.pl (dead) No revisions exist on post-st-migration
pg_make_reaction_tables.pl (dead) No revisions exist on post-st-migration
pg_make_reaction_properties.pl (dead) No revisions exist on post-st-migration
pg_make_md5_families.pl (dead) No revisions exist on post-st-migration
pg_make_initial_models.pl (dead) No revisions exist on post-st-migration
pg_janaka_get_role_reactions_pegs.pl (dead) No revisions exist on post-st-migration
pg_intersection.pl (dead) No revisions exist on post-st-migration
pg_inconsistent_families.pl (dead) No revisions exist on post-st-migration
pg_get_stats.pl (dead) No revisions exist on post-st-migration
pg_get_reactions.pl (dead) No revisions exist on post-st-migration
pg_get_reaction_role.pl (dead) No revisions exist on post-st-migration
pg_get_reaction_keys.pl (dead) No revisions exist on post-st-migration
pg_get_pegs_in_repeats.pl (dead) No revisions exist on post-st-migration
pg_get_models.pl (dead) No revisions exist on post-st-migration
pg_get_gapfill_reactions.pl (dead) No revisions exist on post-st-migration
pg_get_consistency_before_after.pl (dead) No revisions exist on post-st-migration
pg_get_codon_usage_stats.pl (dead) No revisions exist on post-st-migration
pg_generate_possible_assignments.pl (dead) No revisions exist on post-st-migration
pg_function_of.pl (dead) No revisions exist on post-st-migration
pg_form_mobile_element_families.pl (dead) No revisions exist on post-st-migration
pg_filter_alien.pl (dead) No revisions exist on post-st-migration
pg_extract_reaction_sets.pl (dead) No revisions exist on post-st-migration
pg_events.pl (dead) No revisions exist on post-st-migration
pg_estimate_alien_pegs.pl (dead) No revisions exist on post-st-migration
pg_core_families.pl (dead) No revisions exist on post-st-migration
pg_compute_traits.pl (dead) No revisions exist on post-st-migration
pg_compute_subsystem_membership.pl (dead) No revisions exist on post-st-migration
pg_compute_md5s.pl (dead) No revisions exist on post-st-migration
pg_compute_corr.pl (dead) No revisions exist on post-st-migration
pg_check_gapfills.pl (dead) No revisions exist on post-st-migration
pg_build_protein_families.pl (dead) No revisions exist on post-st-migration
pg_build_newick_tree.pl (dead) No revisions exist on post-st-migration
pg_build_fasta_for_phylogeny.pl (dead) No revisions exist on post-st-migration
pg_adjacency_of_core.pl (dead) No revisions exist on post-st-migration
pg_add_role_peg.pl (dead) No revisions exist on post-st-migration
pg_add_genomes.pl (dead) No revisions exist on post-st-migration
pegs_on_contigs.pl (dead) No revisions exist on post-st-migration
pegs_in_subsystems.pl (dead) No revisions exist on post-st-migration
pegs_in_subsystem.pl (dead) No revisions exist on post-st-migration
pegs_in_conflict.pl (dead) No revisions exist on post-st-migration
pegs.pl (dead) No revisions exist on post-st-migration
peg_to_subsystems.pl (dead) No revisions exist on post-st-migration
peg_to_pdb.py (dead) No revisions exist on post-st-migration
peg_to_name.pl (dead) No revisions exist on post-st-migration
peg2pubmed.pl (dead) No revisions exist on post-st-migration
patric_call_proteins.pl (dead) No revisions exist on post-st-migration
partition_prots.pl (dead) No revisions exist on post-st-migration
parse_uniparc.pl (dead) No revisions exist on post-st-migration
parse_mart.py (dead) No revisions exist on post-st-migration
parse_genbank.pl (dead) No revisions exist on post-st-migration
parse_genbank (dead) No revisions exist on post-st-migration
paint_tree.pl (dead) No revisions exist on post-st-migration
paint_reactions_on_tree_pipeline.pl (dead) No revisions exist on post-st-migration
package_translation_rules.pl (dead) No revisions exist on post-st-migration
package_translation_rules (dead) No revisions exist on post-st-migration
package_subsystems.pl (dead) No revisions exist on post-st-migration
package_sims.pl (dead) No revisions exist on post-st-migration
package_raw_data_for_transplant.pl (dead) No revisions exist on post-st-migration
package_lightweight_code.pl (dead) No revisions exist on post-st-migration
package_lightweight_code (dead) No revisions exist on post-st-migration
package_fix.pl (dead) No revisions exist on post-st-migration
package_code.pl (dead) No revisions exist on post-st-migration
package_code (dead) No revisions exist on post-st-migration
package_cleaned_bins.pl (dead) No revisions exist on post-st-migration
package_assignments.pl (dead) No revisions exist on post-st-migration
package_assignments (dead) No revisions exist on post-st-migration
package_annotations.pl (dead) No revisions exist on post-st-migration
package_annotations (dead) No revisions exist on post-st-migration
p3x_kser_parallel_load.pl (dead) No revisions exist on post-st-migration
p3x-write-subsystem-qa.pl (dead) No revisions exist on post-st-migration
p3x-write-family-defs.pl (dead) No revisions exist on post-st-migration
p3x-update-propagated-family-names.pl (dead) No revisions exist on post-st-migration
p3x-test-evaluator.pl (dead) No revisions exist on post-st-migration
p3x-split-families.pl (dead) No revisions exist on post-st-migration
p3x-setup-alignment-sync-dir.pl (dead) No revisions exist on post-st-migration
p3x-reduce-families-for-kser.pl (dead) No revisions exist on post-st-migration
p3x-recall-proteins.pl (dead) No revisions exist on post-st-migration
p3x-recall-patric-proteins.pl (dead) No revisions exist on post-st-migration
p3x-propagate-family-names.pl (dead) No revisions exist on post-st-migration
p3x-eval-sort.pl (dead) No revisions exist on post-st-migration
p3x-eval-gto.pl (dead) No revisions exist on post-st-migration
p3x-eval-genomes.pl (dead) No revisions exist on post-st-migration
p3x-eval-genome.pl (dead) No revisions exist on post-st-migration
p3x-eval-bins.pl (dead) No revisions exist on post-st-migration
p3x-eval-bin-site.pl (dead) No revisions exist on post-st-migration
p3x-create-split-nr-for-fams.pl (dead) No revisions exist on post-st-migration
p3x-create-release-dir.pl (dead) No revisions exist on post-st-migration
p3x-compute-patric-update.pl (dead) No revisions exist on post-st-migration
p3x-compute-patric-update-delta.pl (dead) No revisions exist on post-st-migration
p3x-compare-patric-calls.pl (dead) No revisions exist on post-st-migration
p3x-compare-patric-calls-2.pl (dead) No revisions exist on post-st-migration
p3x-check-mcl-compute-times.pl (dead) No revisions exist on post-st-migration
p3_contigs_in_genome.pl (dead) No revisions exist on post-st-migration
p3_all_genomes.pl (dead) No revisions exist on post-st-migration
p3_all_features.pl (dead) No revisions exist on post-st-migration
p3-write-kmers.pl (dead) No revisions exist on post-st-migration
p3-uni-roles.pl (dead) No revisions exist on post-st-migration
p3-tests.pl (dead) No revisions exist on post-st-migration
p3-tbl-to-html.pl (dead) No revisions exist on post-st-migration
p3-tbl-to-fasta.pl (dead) No revisions exist on post-st-migration
p3-tail.pl (dead) No revisions exist on post-st-migration
p3-subsys-roles.pl (dead) No revisions exist on post-st-migration
p3-stats.pl (dead) No revisions exist on post-st-migration
p3-sort.pl (dead) No revisions exist on post-st-migration
p3-similar-proteins-by-family.pl (dead) No revisions exist on post-st-migration
p3-similar-proteins-by-blast.pl (dead) No revisions exist on post-st-migration
p3-signature-peginfo.pl (dead) No revisions exist on post-st-migration
p3-signature-families.pl (dead) No revisions exist on post-st-migration
p3-signature-clusters.pl (dead) No revisions exist on post-st-migration
p3-set-to-relation.pl (dead) No revisions exist on post-st-migration
p3-sequence-profile.pl (dead) No revisions exist on post-st-migration
p3-role-matrix.pl (dead) No revisions exist on post-st-migration
p3-role-features.pl (dead) No revisions exist on post-st-migration
p3-rep-prots.pl (dead) No revisions exist on post-st-migration
p3-related-by-clusters.pl (dead) No revisions exist on post-st-migration
p3-rast.pl (dead) No revisions exist on post-st-migration
p3-put-genome-group.pl (dead) No revisions exist on post-st-migration
p3-put-feature-group.pl (dead) No revisions exist on post-st-migration
p3-project-subsystems.pl (dead) No revisions exist on post-st-migration
p3-pick.pl (dead) No revisions exist on post-st-migration
p3-merge.pl (dead) No revisions exist on post-st-migration
p3-match.pl (dead) No revisions exist on post-st-migration
p3-mass-cluster-run.pl (dead) No revisions exist on post-st-migration
p3-login.pl (dead) No revisions exist on post-st-migration
p3-list-genome-groups.pl (dead) No revisions exist on post-st-migration
p3-list-feature-groups.pl (dead) No revisions exist on post-st-migration
p3-kmer-compare.pl (dead) No revisions exist on post-st-migration
p3-join.pl (dead) No revisions exist on post-st-migration
p3-inAorB.pl (dead) No revisions exist on post-st-migration
p3-inAnotB.pl (dead) No revisions exist on post-st-migration
p3-inAandB.pl (dead) No revisions exist on post-st-migration
p3-identify-clusters.pl (dead) No revisions exist on post-st-migration
p3-identical-proteins.pl (dead) No revisions exist on post-st-migration
p3-identical-dna.pl (dead) No revisions exist on post-st-migration
p3-head.pl (dead) No revisions exist on post-st-migration
p3-gto.pl (dead) No revisions exist on post-st-migration
p3-gto-scan.pl (dead) No revisions exist on post-st-migration
p3-gto-fasta.pl (dead) No revisions exist on post-st-migration
p3-gto-dna.pl (dead) No revisions exist on post-st-migration
p3-get-genome-subsystems.pl (dead) No revisions exist on post-st-migration
p3-get-genome-group.pl (dead) No revisions exist on post-st-migration
p3-get-genome-features.pl (dead) No revisions exist on post-st-migration
p3-get-genome-expression.pl (dead) No revisions exist on post-st-migration
p3-get-genome-drugs.pl (dead) No revisions exist on post-st-migration
p3-get-genome-data.pl (dead) No revisions exist on post-st-migration
p3-get-genome-contigs.pl (dead) No revisions exist on post-st-migration
p3-get-features-by-sequence.pl (dead) No revisions exist on post-st-migration
p3-get-feature-subsystems.pl (dead) No revisions exist on post-st-migration
p3-get-feature-sequence.pl (dead) No revisions exist on post-st-migration
p3-get-feature-regions.pl (dead) No revisions exist on post-st-migration
p3-get-feature-group.pl (dead) No revisions exist on post-st-migration
p3-get-feature-data.pl (dead) No revisions exist on post-st-migration
p3-get-family-features.pl (dead) No revisions exist on post-st-migration
p3-get-family-data.pl (dead) No revisions exist on post-st-migration
p3-get-drug-genomes.pl (dead) No revisions exist on post-st-migration
p3-get-contig-data.pl (dead) No revisions exist on post-st-migration
p3-genus-species.pl (dead) No revisions exist on post-st-migration
p3-genome-kmer-hits.pl (dead) No revisions exist on post-st-migration
p3-genome-fasta.pl (dead) No revisions exist on post-st-migration
p3-genome-distance.pl (dead) No revisions exist on post-st-migration
p3-genome-amr-data.pl (dead) No revisions exist on post-st-migration
p3-generate-clusters.pl (dead) No revisions exist on post-st-migration
p3-generate-close-roles.pl (dead) No revisions exist on post-st-migration
p3-function-to-role.pl (dead) No revisions exist on post-st-migration
p3-function-parse.pl (dead) No revisions exist on post-st-migration
p3-format-results.pl (dead) No revisions exist on post-st-migration
p3-find-in-clusters.pl (dead) No revisions exist on post-st-migration
p3-find-features.pl (dead) No revisions exist on post-st-migration
p3-find-couples.pl (dead) No revisions exist on post-st-migration
p3-file-filter.pl (dead) No revisions exist on post-st-migration
p3-feature-upstream.pl (dead) No revisions exist on post-st-migration
p3-feature-gap.pl (dead) No revisions exist on post-st-migration
p3-extract.pl (dead) No revisions exist on post-st-migration
p3-extract-gto.pl (dead) No revisions exist on post-st-migration
p3-echo.pl (dead) No revisions exist on post-st-migration
p3-drug-amr-data.pl (dead) No revisions exist on post-st-migration
p3-discriminating-kmers.pl (dead) No revisions exist on post-st-migration
p3-count.pl (dead) No revisions exist on post-st-migration
p3-count-families.pl (dead) No revisions exist on post-st-migration
p3-collate.pl (dead) No revisions exist on post-st-migration
p3-co-occur.pl (dead) No revisions exist on post-st-migration
p3-closest-seqs.pl (dead) No revisions exist on post-st-migration
p3-build-kmer-db.pl (dead) No revisions exist on post-st-migration
p3-blast.pl (dead) No revisions exist on post-st-migration
p3-all-taxonomies.pl (dead) No revisions exist on post-st-migration
p3-all-subsystems.pl (dead) No revisions exist on post-st-migration
p3-all-genomes.pl (dead) No revisions exist on post-st-migration
p3-all-drugs.pl (dead) No revisions exist on post-st-migration
p3-aggregates-to-html.pl (dead) No revisions exist on post-st-migration
p3-aggregate-sss.pl (dead) No revisions exist on post-st-migration
p3-abstract-clusters.pl (dead) No revisions exist on post-st-migration
p2p_sync_from_remote.pl (dead) No revisions exist on post-st-migration
p2p_sync_cron.pl (dead) No revisions exist on post-st-migration
p2p_daemon.pl (dead) No revisions exist on post-st-migration
overlap_resolution_test.pl (dead) No revisions exist on post-st-migration
order_sets.pl (dead) No revisions exist on post-st-migration
order_seqs_on_length.pl (dead) No revisions exist on post-st-migration
order_figfams.pl (dead) No revisions exist on post-st-migration
order_corrections_for_start_predictions.pl (dead) No revisions exist on post-st-migration
nmpdr2gff.pl (dead) No revisions exist on post-st-migration
new_versions_of_features.pl (dead) No revisions exist on post-st-migration
native_codon_usage.pl (dead) No revisions exist on post-st-migration
nap.c (dead) No revisions exist on post-st-migration
myjoin.pl (dead) No revisions exist on post-st-migration
modify_tree.pl (dead) No revisions exist on post-st-migration
modelCompare.pl (dead) No revisions exist on post-st-migration
modal_codon_usage.pl (dead) No revisions exist on post-st-migration
mg_user_id_to_unique.pl (dead) No revisions exist on post-st-migration
metagenome2genbank.pl (dead) No revisions exist on post-st-migration
metabolic_reconstruction.pl (dead) No revisions exist on post-st-migration
meta.pl (dead) No revisions exist on post-st-migration
merge_translation_rules.pl (dead) No revisions exist on post-st-migration
merge_translation_rules (dead) No revisions exist on post-st-migration
merge_peg_synonyms.pl (dead) No revisions exist on post-st-migration
merge_missing_sims.pl (dead) No revisions exist on post-st-migration
merge_missing_gene_output.pl (dead) No revisions exist on post-st-migration
merge_gene_sets.pl (dead) No revisions exist on post-st-migration
merge_families.pl (dead) No revisions exist on post-st-migration
merge_assignments.pl (dead) No revisions exist on post-st-migration
merge_annotations.pl (dead) No revisions exist on post-st-migration
merge_annotations (dead) No revisions exist on post-st-migration
md5.c (dead) No revisions exist on post-st-migration
match_to_genome_frequencies.pl (dead) No revisions exist on post-st-migration
match_to_genome_axes.pl (dead) No revisions exist on post-st-migration
match_to_axes.pl (dead) No revisions exist on post-st-migration
match_dna_to_aligned_prots.pl (dead) No revisions exist on post-st-migration
mark_picked_genes.pl (dead) No revisions exist on post-st-migration
mark_nr.pl (dead) No revisions exist on post-st-migration
mark_genome_as_phage.pl (dead) No revisions exist on post-st-migration
map_to_scaffold.pl (dead) No revisions exist on post-st-migration
map_sims_for_bigfc.pl (dead) No revisions exist on post-st-migration
map_sims.pl (dead) No revisions exist on post-st-migration
map_pegs.pl (dead) No revisions exist on post-st-migration
map_pegs (dead) No revisions exist on post-st-migration
map-nr-ids-to-ncbi-std.pl (dead) No revisions exist on post-st-migration
make_uniprot_corr.pl (dead) No revisions exist on post-st-migration
make_trimmed_alignment_from_ids.pl (dead) No revisions exist on post-st-migration
make_transferable_tarfiles.pl (dead) No revisions exist on post-st-migration
make_transferable_chunks.pl (dead) No revisions exist on post-st-migration
make_transferable_chunks (dead) No revisions exist on post-st-migration
make_timestamps.pl (dead) No revisions exist on post-st-migration
make_tf_equivalog_file.pl (dead) No revisions exist on post-st-migration
make_supporting_predicates.pl (dead) No revisions exist on post-st-migration
make_subsystems_from_clusters.pl (dead) No revisions exist on post-st-migration
make_subsys_based_families2.pl (dead) No revisions exist on post-st-migration
make_subsys_based_families.pl (dead) No revisions exist on post-st-migration
make_sr_inconsistent_fams.pl (dead) No revisions exist on post-st-migration
make_sprout_upstream.pl (dead) No revisions exist on post-st-migration
make_sprout_bbhs.pl (dead) No revisions exist on post-st-migration
make_spreadsheet_and_notes.pl (dead) No revisions exist on post-st-migration
make_sp_uni_files.pl (dead) No revisions exist on post-st-migration
make_sp_org_table.pl (dead) No revisions exist on post-st-migration
make_sp_org_domain_table.pl (dead) No revisions exist on post-st-migration
make_sp_func_syn_dicts.pl (dead) No revisions exist on post-st-migration
make_sp_desc_with_org.pl (dead) No revisions exist on post-st-migration
make_sims_and_fc_data.pl (dead) No revisions exist on post-st-migration
make_sim_tab.pl (dead) No revisions exist on post-st-migration
make_sim_sets.pl (dead) No revisions exist on post-st-migration
make_sim_sets (dead) No revisions exist on post-st-migration
make_sim_part_data.pl (dead) No revisions exist on post-st-migration
make_scored_instances.pl (dead) No revisions exist on post-st-migration
make_release.pl (dead) No revisions exist on post-st-migration
make_reduce_sims_index.pl (dead) No revisions exist on post-st-migration
make_reaction_network.pl (dead) No revisions exist on post-st-migration
make_rates.pl (dead) No revisions exist on post-st-migration
make_pu_from_seqs.pl (dead) No revisions exist on post-st-migration
make_pu_from_ids.pl (dead) No revisions exist on post-st-migration
make_protein_weights_and_rates.pl (dead) No revisions exist on post-st-migration
make_protein_sets.pl (dead) No revisions exist on post-st-migration
make_protein_sets (dead) No revisions exist on post-st-migration
make_prosite_ontology.pl (dead) No revisions exist on post-st-migration
make_proposed_assignments_for_consistency.pl (dead) No revisions exist on post-st-migration
make_proml_tree_2.pl (dead) No revisions exist on post-st-migration
make_proml_tree_0.pl (dead) No revisions exist on post-st-migration
make_proml_tree.pl (dead) No revisions exist on post-st-migration
make_probes_to_genes.pl (dead) No revisions exist on post-st-migration
make_predictor_input_from_gto.pl (dead) No revisions exist on post-st-migration
make_predictor_input.pl (dead) No revisions exist on post-st-migration
make_pir_ontology.pl (dead) No revisions exist on post-st-migration
make_phob_from_seqs.pl (dead) No revisions exist on post-st-migration
make_phob_from_ids.pl (dead) No revisions exist on post-st-migration
make_pfam_ontology.pl (dead) No revisions exist on post-st-migration
make_peg_maps_from_fasta.pl (dead) No revisions exist on post-st-migration
make_peg_maps.pl (dead) No revisions exist on post-st-migration
make_peg_map_from_tbl.pl (dead) No revisions exist on post-st-migration
make_pdb_ontology.pl (dead) No revisions exist on post-st-migration
make_partition_reps_worker.pl (dead) No revisions exist on post-st-migration
make_partition_repsW.pl (dead) No revisions exist on post-st-migration
make_partition_repsP.pl (dead) No revisions exist on post-st-migration
make_partition_reps.pl (dead) No revisions exist on post-st-migration
make_parallel_proml_run.pl (dead) No revisions exist on post-st-migration
make_overlap_report.pl (dead) No revisions exist on post-st-migration
make_occ_counts.pl (dead) No revisions exist on post-st-migration
make_occ_counts (dead) No revisions exist on post-st-migration
make_neigh_joining_tree.pl (dead) No revisions exist on post-st-migration
make_ncbi_files.pl (dead) No revisions exist on post-st-migration
make_model_spreadsheets.pl (dead) No revisions exist on post-st-migration
make_md5_figfams_file.pl (dead) No revisions exist on post-st-migration
make_match_table.pl (dead) No revisions exist on post-st-migration
make_maps_from_sub.py (dead) No revisions exist on post-st-migration
make_ma_html.pl (dead) No revisions exist on post-st-migration
make_kegg_files.pl (dead) No revisions exist on post-st-migration
make_kb_md5.pl (dead) No revisions exist on post-st-migration
make_jpg.pl (dead) No revisions exist on post-st-migration
make_interpro_ontology.pl (dead) No revisions exist on post-st-migration
make_initial_partition_scores.pl (dead) No revisions exist on post-st-migration
make_indexes.pl (dead) No revisions exist on post-st-migration
make_indexes (dead) No revisions exist on post-st-migration
make_go_ontology.pl (dead) No revisions exist on post-st-migration
make_genome_dir_for_close.pl (dead) No revisions exist on post-st-migration
make_final_condensed_bbhs.pl (dead) No revisions exist on post-st-migration
make_figfams.pl (dead) No revisions exist on post-st-migration
make_figfam_tree_worker.pl (dead) No revisions exist on post-st-migration
make_figfam_tree.pl (dead) No revisions exist on post-st-migration
make_fig_files.pl (dead) No revisions exist on post-st-migration
make_fasta_btree.pl (dead) No revisions exist on post-st-migration
make_fam_tabs.pl (dead) No revisions exist on post-st-migration
make_external_sequence_data.pl (dead) No revisions exist on post-st-migration
make_coreg_conjectures_based_on_subsys.pl (dead) No revisions exist on post-st-migration
make_close_strain_family_tabs.pl (dead) No revisions exist on post-st-migration
make_close_strain_data.pl (dead) No revisions exist on post-st-migration
make_close.pl (dead) No revisions exist on post-st-migration
make_cdd_ontology.pl (dead) No revisions exist on post-st-migration
make_calls_for_start_predictions.pl (dead) No revisions exist on post-st-migration
make_calls.pl (dead) No revisions exist on post-st-migration
make_calls (dead) No revisions exist on post-st-migration
make_binary.pl (dead) No revisions exist on post-st-migration
make_binary (dead) No revisions exist on post-st-migration
make_attribute_index.pl (dead) No revisions exist on post-st-migration
make_assignments_set.pl (dead) No revisions exist on post-st-migration
make_assignments_fit_initial_css.pl (dead) No revisions exist on post-st-migration
make_assertions_from_uploads.pl (dead) No revisions exist on post-st-migration
make_annotations_for_sprout.pl (dead) No revisions exist on post-st-migration
make_SignalP_attributes.pl (dead) No revisions exist on post-st-migration
make_SBML_model.pl (dead) No revisions exist on post-st-migration
make_Phobius_attributes.pl (dead) No revisions exist on post-st-migration
make_PROSITE_PIR_PRODOM_attributes.pl (dead) No revisions exist on post-st-migration
make_PHOBs_for_subsystems.pl (dead) No revisions exist on post-st-migration
make_PG.pl (dead) No revisions exist on post-st-migration
make_PG (dead) No revisions exist on post-st-migration
make_PFAM_HMM_derived_attributes.pl (dead) No revisions exist on post-st-migration
make_PDB_attributes.pl (dead) No revisions exist on post-st-migration
make_PATRICfams_collapse_md5.pl (dead) No revisions exist on post-st-migration
make_PATRICfams.pl (dead) No revisions exist on post-st-migration
make_Ontology_database.pl (dead) No revisions exist on post-st-migration
make_MPS_model_v2.pl (dead) No revisions exist on post-st-migration
make_MPS_model.pl (dead) No revisions exist on post-st-migration
make_MFA_tool_input.pl (dead) No revisions exist on post-st-migration
make_IPR_PFAM_GO_attributes.pl (dead) No revisions exist on post-st-migration
make_FigFamsData.pl (dead) No revisions exist on post-st-migration
make_FIG_annotations_for_sprout.pl (dead) No revisions exist on post-st-migration
make_CELLO_and_TMPRED_attributes.pl (dead) No revisions exist on post-st-migration
make_CDD_attributes.pl (dead) No revisions exist on post-st-migration
maint-remove-obsolete-aliases.pl (dead) No revisions exist on post-st-migration
macapp_files_to_genome_dir.pl (dead) No revisions exist on post-st-migration
ma_pipeline_shewanella.pl (dead) No revisions exist on post-st-migration
ma_pipeline_ecoli.pl (dead) No revisions exist on post-st-migration
ma_pipeline.pl (dead) No revisions exist on post-st-migration
ma.cgi (dead) No revisions exist on post-st-migration
location_of.pl (dead) No revisions exist on post-st-migration
load_wikipedia.pl (dead) No revisions exist on post-st-migration
load_ss_classification.pl (dead) No revisions exist on post-st-migration
load_sprout.pl (dead) No revisions exist on post-st-migration
load_sims.pl (dead) No revisions exist on post-st-migration
load_sets.pl (dead) No revisions exist on post-st-migration
load_sets (dead) No revisions exist on post-st-migration
load_protein_families.pl (dead) No revisions exist on post-st-migration
load_protein_families (dead) No revisions exist on post-st-migration
load_propagation_locks.pl (dead) No revisions exist on post-st-migration
load_pirsf.pl (dead) No revisions exist on post-st-migration
load_peg_mapping.pl (dead) No revisions exist on post-st-migration
load_peg_mapping (dead) No revisions exist on post-st-migration
load_pch_pins.pl (dead) No revisions exist on post-st-migration
load_pch_pins (dead) No revisions exist on post-st-migration
load_pattyfams.pl (dead) No revisions exist on post-st-migration
load_patric_map.pl (dead) No revisions exist on post-st-migration
load_md5_alignment.pl (dead) No revisions exist on post-st-migration
load_locks.pl (dead) No revisions exist on post-st-migration
load_local_maps.pl (dead) No revisions exist on post-st-migration
load_literature.pl (dead) No revisions exist on post-st-migration
load_links.pl (dead) No revisions exist on post-st-migration
load_kmers_into_memcache.pl (dead) No revisions exist on post-st-migration
load_kmer_peg_db.pl (dead) No revisions exist on post-st-migration
load_kegg.pl (dead) No revisions exist on post-st-migration
load_kegg (dead) No revisions exist on post-st-migration
load_id_correspondence.pl (dead) No revisions exist on post-st-migration
load_hugo.pl (dead) No revisions exist on post-st-migration
load_go.pl (dead) No revisions exist on post-st-migration
load_function_transition_table.pl (dead) No revisions exist on post-st-migration
load_features.pl (dead) No revisions exist on post-st-migration
load_features (dead) No revisions exist on post-st-migration
load_external_orgs.pl (dead) No revisions exist on post-st-migration
load_external_orgs (dead) No revisions exist on post-st-migration
load_ec_names.pl (dead) No revisions exist on post-st-migration
load_ec_names (dead) No revisions exist on post-st-migration
load_dlits.pl (dead) No revisions exist on post-st-migration
load_distances.pl (dead) No revisions exist on post-st-migration
load_coupling_btree.pl (dead) No revisions exist on post-st-migration
load_coupling.pl (dead) No revisions exist on post-st-migration
load_close.pl (dead) No revisions exist on post-st-migration
load_chromosomal_clusters.pl (dead) No revisions exist on post-st-migration
load_chromosomal_clusters (dead) No revisions exist on post-st-migration
load_bbhs_btree.pl (dead) No revisions exist on post-st-migration
load_bbhs.pl (dead) No revisions exist on post-st-migration
load_attributes.pl (dead) No revisions exist on post-st-migration
load_atomic_regulons.pl (dead) No revisions exist on post-st-migration
load_abstract_coupling.pl (dead) No revisions exist on post-st-migration
load_ACH_resolution_DB.pl (dead) No revisions exist on post-st-migration
list_genomes.pl (dead) No revisions exist on post-st-migration
list_genomes (dead) No revisions exist on post-st-migration
lengths_of_contigs.pl (dead) No revisions exist on post-st-migration
lengths_of_contigs (dead) No revisions exist on post-st-migration
label_all_nodes.pl (dead) No revisions exist on post-st-migration
kp_run_tests.pl (dead) No revisions exist on post-st-migration
kp_process_hits.pl (dead) No revisions exist on post-st-migration
kp_process_dna_hits.pl (dead) No revisions exist on post-st-migration
kp_get_properties_next_round.pl (dead) No revisions exist on post-st-migration
kp_build_Data.pl (dead) No revisions exist on post-st-migration
kmer_search.pl (dead) No revisions exist on post-st-migration
kmer_property_search.pl (dead) No revisions exist on post-st-migration
kmer_guts_net.pl (dead) No revisions exist on post-st-migration
kmer_classifier.pl (dead) No revisions exist on post-st-migration
kmc (dead) No revisions exist on post-st-migration
km_process_hits_to_regions.pl (dead) No revisions exist on post-st-migration
km_pick_best_hit_in_peg.pl (dead) No revisions exist on post-st-migration
km_build_kmers_part2.pl (dead) No revisions exist on post-st-migration
km_build_kmers_part1.pl (dead) No revisions exist on post-st-migration
km_build_just_otu_index.pl (dead) No revisions exist on post-st-migration
km_build_function_index.pl (dead) No revisions exist on post-st-migration
km_build_Data.pl (dead) No revisions exist on post-st-migration
keep_only.pl (dead) No revisions exist on post-st-migration
keep_good_connections.pl (dead) No revisions exist on post-st-migration
k-class-tree-from-contig-dir.pl (dead) No revisions exist on post-st-migration
k-class-representative_n_tree_tips.pl (dead) No revisions exist on post-st-migration
k-class-kc.pl (dead) No revisions exist on post-st-migration
k-class-get-bork-universals.pl (dead) No revisions exist on post-st-migration
k-class-get-adaboost-tree-tips.pl (dead) No revisions exist on post-st-migration
k-class-adaboost.pl (dead) No revisions exist on post-st-migration
k-class-adaboost-matrix-parallel.pl (dead) No revisions exist on post-st-migration
k-class-adaboost-classify.pl (dead) No revisions exist on post-st-migration
k-class-PSEED-kc.pl (dead) No revisions exist on post-st-migration
just_inconsistent_sets.pl (dead) No revisions exist on post-st-migration
jgi_data_merge.pl (dead) No revisions exist on post-st-migration
janaka_pipeline.pl (dead) No revisions exist on post-st-migration
is_prokaryotic.pl (dead) No revisions exist on post-st-migration
is_eukaryotic.pl (dead) No revisions exist on post-st-migration
is_bacterial.pl (dead) No revisions exist on post-st-migration
is_archaeal.pl (dead) No revisions exist on post-st-migration
interval.pl (dead) No revisions exist on post-st-migration
install_translation_rules.pl (dead) No revisions exist on post-st-migration
install_translation_rules (dead) No revisions exist on post-st-migration
install_subsystems.pl (dead) No revisions exist on post-st-migration
install_rast_batch.pl (dead) No revisions exist on post-st-migration
install_partitions.pl (dead) No revisions exist on post-st-migration
install_partition_reps.pl (dead) No revisions exist on post-st-migration
install_new_coupling_data.pl (dead) No revisions exist on post-st-migration
install_lightweight_code.pl (dead) No revisions exist on post-st-migration
install_lightweight_code (dead) No revisions exist on post-st-migration
install_features_batch.pl (dead) No revisions exist on post-st-migration
install_feature_updates.pl (dead) No revisions exist on post-st-migration
install_code.pl (dead) No revisions exist on post-st-migration
install_code (dead) No revisions exist on post-st-migration
install_assignments.pl (dead) No revisions exist on post-st-migration
install_assignments (dead) No revisions exist on post-st-migration
install_anticipated_functions.pl (dead) No revisions exist on post-st-migration
install_annotations.pl (dead) No revisions exist on post-st-migration
install_annotations (dead) No revisions exist on post-st-migration
install-data.pl (dead) No revisions exist on post-st-migration
insert_prot_into_tree.pl (dead) No revisions exist on post-st-migration
insert_into_a_tree.pl (dead) No revisions exist on post-st-migration
insert_all.pl (dead) No revisions exist on post-st-migration
insert.pl (dead) No revisions exist on post-st-migration
initialize_figfams.pl (dead) No revisions exist on post-st-migration
initialize_ann_and_ev.pl (dead) No revisions exist on post-st-migration
initialize_alignments_for_subsystems.pl (dead) No revisions exist on post-st-migration
initial_set.pl (dead) No revisions exist on post-st-migration
init_peg_job_scheduler.pl (dead) No revisions exist on post-st-migration
init_maps.pl (dead) No revisions exist on post-st-migration
init_dbserver.pl (dead) No revisions exist on post-st-migration
init_FIG.pl (dead) No revisions exist on post-st-migration
init_FIG (dead) No revisions exist on post-st-migration
indirect_functional_coupling_mcauliffe.pl (dead) No revisions exist on post-st-migration
indirect_functional_coupling.pl (dead) No revisions exist on post-st-migration
index_translations_MD5.pl (dead) No revisions exist on post-st-migration
index_translations.pl (dead) No revisions exist on post-st-migration
index_translations (dead) No revisions exist on post-st-migration
index_translation_files.c (dead) No revisions exist on post-st-migration
index_subsystems.pl (dead) No revisions exist on post-st-migration
index_sprout.pl (dead) No revisions exist on post-st-migration
index_sims_file.c (dead) No revisions exist on post-st-migration
index_sims.pl (dead) No revisions exist on post-st-migration
index_sims (dead) No revisions exist on post-st-migration
index_pins.pl (dead) No revisions exist on post-st-migration
index_nr.pl (dead) No revisions exist on post-st-migration
index_neighborhoods.pl (dead) No revisions exist on post-st-migration
index_neighborhoods (dead) No revisions exist on post-st-migration
index_genome.pl (dead) No revisions exist on post-st-migration
index_figv_annos.pl (dead) No revisions exist on post-st-migration
index_feature_dir_fasta.pl (dead) No revisions exist on post-st-migration
index_fasta.pl (dead) No revisions exist on post-st-migration
index_contigs.pl (dead) No revisions exist on post-st-migration
index_contigs (dead) No revisions exist on post-st-migration
index_contig_files.c (dead) No revisions exist on post-st-migration
index_annotations.pl (dead) No revisions exist on post-st-migration
index_annotations (dead) No revisions exist on post-st-migration
index_anno_clearinghouse.pl (dead) No revisions exist on post-st-migration
index-pegsyn2.pl (dead) No revisions exist on post-st-migration
index-pegsyn.pl (dead) No revisions exist on post-st-migration
import_subsystems.pl (dead) No revisions exist on post-st-migration
import_similarity_bundle.pl (dead) No revisions exist on post-st-migration
import_external_sequences_step3.pl (dead) No revisions exist on post-st-migration
import_external_sequences_step1.pl (dead) No revisions exist on post-st-migration
iedb.pl (dead) No revisions exist on post-st-migration
identify_organism.pl (dead) No revisions exist on post-st-migration
ic50_extract.pl (dead) No revisions exist on post-st-migration
ic50_compare.pl (dead) No revisions exist on post-st-migration
html_parser.py (dead) No revisions exist on post-st-migration
harvest_genomes_from_samples.pl (dead) No revisions exist on post-st-migration
gto_to_tbl.pl (dead) No revisions exist on post-st-migration
gto_crisprs.pl (dead) No revisions exist on post-st-migration
gto_complete_check.pl (dead) No revisions exist on post-st-migration
gset-initdb.pl (dead) No revisions exist on post-st-migration
glue_tbl_to_metabolic_reconstruction.pl (dead) No revisions exist on post-st-migration
gjoseqlib.h (dead) No revisions exist on post-st-migration
gjoseqlib.c (dead) No revisions exist on post-st-migration
gjoseqio.h (dead) No revisions exist on post-st-migration
gjoseqio.c (dead) No revisions exist on post-st-migration
gjocodonlib.h (dead) No revisions exist on post-st-migration
gjocodonlib.c (dead) No revisions exist on post-st-migration
gi2fig.pl (dead) No revisions exist on post-st-migration
gff_statistics.pl (dead) No revisions exist on post-st-migration
gff2tab.pl (dead) No revisions exist on post-st-migration
gff2seed.pl (dead) No revisions exist on post-st-migration
gff2ncbitab.pl (dead) No revisions exist on post-st-migration
gff2Ontology.pl (dead) No revisions exist on post-st-migration
get_unique_kmers_for_rnaseq.pl (dead) No revisions exist on post-st-migration
get_translations_for_genomes.pl (dead) No revisions exist on post-st-migration
get_translations.pl (dead) No revisions exist on post-st-migration
get_taxid_journals.pl (dead) No revisions exist on post-st-migration
get_synonyms_from_ach_for_id.pl (dead) No revisions exist on post-st-migration
get_subsystem_properties.pl (dead) No revisions exist on post-st-migration
get_ss_connections.pl (dead) No revisions exist on post-st-migration
get_sims_for_start_predictions.pl (dead) No revisions exist on post-st-migration
get_rna_features_for_calling_genes.pl (dead) No revisions exist on post-st-migration
get_rid_of_small_or_too_many_per_FF.pl (dead) No revisions exist on post-st-migration
get_recent_annotations.pl (dead) No revisions exist on post-st-migration
get_pubmed_journals.pl (dead) No revisions exist on post-st-migration
get_potential_starts_for_start_predictions.pl (dead) No revisions exist on post-st-migration
get_peg_md5_func_subsystem.pl (dead) No revisions exist on post-st-migration
get_pathways_for_EC.pl (dead) No revisions exist on post-st-migration
get_pairs.pl (dead) No revisions exist on post-st-migration
get_nr_entries_without_sims.pl (dead) No revisions exist on post-st-migration
get_neighbors_and_corr_to_ref.pl (dead) No revisions exist on post-st-migration
get_needed_corr.pl (dead) No revisions exist on post-st-migration
get_merged_families_3.pl (dead) No revisions exist on post-st-migration
get_merged_families_2.pl (dead) No revisions exist on post-st-migration
get_long_enough.pl (dead) No revisions exist on post-st-migration
get_list_of_genomes_to_delete.pl (dead) No revisions exist on post-st-migration
get_journals_for_org.pl (dead) No revisions exist on post-st-migration
get_journals_for_frole.pl (dead) No revisions exist on post-st-migration
get_id_mapping_for_list_of_IDs.pl (dead) No revisions exist on post-st-migration
get_genomes_from_ncbi.pl (dead) No revisions exist on post-st-migration
get_genome_object_from_seed.pl (dead) No revisions exist on post-st-migration
get_figfam_funcs.pl (dead) No revisions exist on post-st-migration
get_fasta_for_tbl_entries.pl (dead) No revisions exist on post-st-migration
get_fasta_for_tbl_entries (dead) No revisions exist on post-st-migration
get_families_kmcl.pl (dead) No revisions exist on post-st-migration
get_families_final.pl (dead) No revisions exist on post-st-migration
get_families_4.pl (dead) No revisions exist on post-st-migration
get_families_3.pl (dead) No revisions exist on post-st-migration
get_families_2.pl (dead) No revisions exist on post-st-migration
get_families_1.pl (dead) No revisions exist on post-st-migration
get_families.pl (dead) No revisions exist on post-st-migration
get_fam_rel.pl (dead) No revisions exist on post-st-migration
get_fam_corr.pl (dead) No revisions exist on post-st-migration
get_exemplars_as_needed.pl (dead) No revisions exist on post-st-migration
get_evaluation_check_rast_new_vs_old.pl (dead) No revisions exist on post-st-migration
get_evaluation_check.pl (dead) No revisions exist on post-st-migration
get_ev_codes.pl (dead) No revisions exist on post-st-migration
get_empty_ecs.pl (dead) No revisions exist on post-st-migration
get_empty_ecs (dead) No revisions exist on post-st-migration
get_dna.pl (dead) No revisions exist on post-st-migration
get_dna (dead) No revisions exist on post-st-migration
get_dlit_data.pl (dead) No revisions exist on post-st-migration
get_coupling_values.pl (dead) No revisions exist on post-st-migration
get_core_PGFs.pl (dead) No revisions exist on post-st-migration
get_close_pegs_kmer_memcache.pl (dead) No revisions exist on post-st-migration
get_close_pegs.pl (dead) No revisions exist on post-st-migration
get_class_examples.pl (dead) No revisions exist on post-st-migration
get_best_set_of_genes_for_column.pl (dead) No revisions exist on post-st-migration
get_all_dlits.pl (dead) No revisions exist on post-st-migration
get_all_annotations.pl (dead) No revisions exist on post-st-migration
get_all.pl (dead) No revisions exist on post-st-migration
get_PSEED_assignment_updates.pl (dead) No revisions exist on post-st-migration
get_PATRIC_AMR_genome_list.pl (dead) No revisions exist on post-st-migration
get_PATRIC_AMR_data.pl (dead) No revisions exist on post-st-migration
get_ON_probes.pl (dead) No revisions exist on post-st-migration
get_NCBI_genome_attributes.pl (dead) No revisions exist on post-st-migration
get_FIGfams_SS_NMPDR_stats.pl (dead) No revisions exist on post-st-migration
genomes_with_essentiality_data.pl (dead) No revisions exist on post-st-migration
genomes_of.pl (dead) No revisions exist on post-st-migration
genome_set.t (dead) No revisions exist on post-st-migration
genome_peg_dna.pl (dead) No revisions exist on post-st-migration
generate_subsys_tables_for_sprout.pl (dead) No revisions exist on post-st-migration
generate_sprout_links.pl (dead) No revisions exist on post-st-migration
generate_similarities.pl (dead) No revisions exist on post-st-migration
generate_similarities (dead) No revisions exist on post-st-migration
generate_prolog_facts.pl (dead) No revisions exist on post-st-migration
generate_pinned_homologs.pl (dead) No revisions exist on post-st-migration
generate_pinned_homologs (dead) No revisions exist on post-st-migration
generate_pin_caches.pl (dead) No revisions exist on post-st-migration
generate_picked.pl (dead) No revisions exist on post-st-migration
generate_partitions_worker.pl (dead) No revisions exist on post-st-migration
generate_partitionsP.pl (dead) No revisions exist on post-st-migration
generate_max_clusters.pl (dead) No revisions exist on post-st-migration
generate_kmer_peg_rel.pl (dead) No revisions exist on post-st-migration
generate_kernel_css.pl (dead) No revisions exist on post-st-migration
generate_kegg_map_ec_tables.pl (dead) No revisions exist on post-st-migration
generate_intergenic_blocks.pl (dead) No revisions exist on post-st-migration
generate_input_for_auto_assignments.pl (dead) No revisions exist on post-st-migration
generate_input_for_auto_assignments (dead) No revisions exist on post-st-migration
generate_ilits.pl (dead) No revisions exist on post-st-migration
generate_ilit_ev_codes.pl (dead) No revisions exist on post-st-migration
generate_genome_feature_tables_for_sprout.pl (dead) No revisions exist on post-st-migration
generate_gene_blocks.pl (dead) No revisions exist on post-st-migration
generate_dlit_ev_codes.pl (dead) No revisions exist on post-st-migration
generate_comparisons.pl (dead) No revisions exist on post-st-migration
generate_clusters.pl (dead) No revisions exist on post-st-migration
generate_all_bbhs.pl (dead) No revisions exist on post-st-migration
generate_SproutData.pl (dead) No revisions exist on post-st-migration
generate_Source_for_sprout.pl (dead) No revisions exist on post-st-migration
generate_Property_for_sprout.pl (dead) No revisions exist on post-st-migration
generate_GenomeGroups_for_sprout.pl (dead) No revisions exist on post-st-migration
generate_GO_attributes.pl (dead) No revisions exist on post-st-migration
genbank2gff3.pl (dead) No revisions exist on post-st-migration
genbank2fasta.pl (dead) No revisions exist on post-st-migration
gd_tree.pl (dead) No revisions exist on post-st-migration
gather_pg_sets.pl (dead) No revisions exist on post-st-migration
gather_genome_info.pl (dead) No revisions exist on post-st-migration
gather_attributes.pl (dead) No revisions exist on post-st-migration
fusion_of.pl (dead) No revisions exist on post-st-migration
functionally_coupled.pl (dead) No revisions exist on post-st-migration
function_of.pl (dead) No revisions exist on post-st-migration
freqs_2_nj_tree.pl (dead) No revisions exist on post-st-migration
freqs_2_dists.pl (dead) No revisions exist on post-st-migration
fq_to_fa.pl (dead) No revisions exist on post-st-migration
format_peg_dbs.pl (dead) No revisions exist on post-st-migration
format_partition_dbs.pl (dead) No revisions exist on post-st-migration
form_clusters.pl (dead) No revisions exist on post-st-migration
flip_sims.pl (dead) No revisions exist on post-st-migration
flattened_to_fasta.pl (dead) No revisions exist on post-st-migration
flatten_fasta.pl (dead) No revisions exist on post-st-migration
flatten_erdb_xml.pl (dead) No revisions exist on post-st-migration
flatten_attribute_files.pl (dead) No revisions exist on post-st-migration
fix_sprout_annotation_relations.pl (dead) No revisions exist on post-st-migration
fix_invalid_fasta.pl (dead) No revisions exist on post-st-migration
fix_ext_funcs.pl (dead) No revisions exist on post-st-migration
fix_eol.pl (dead) No revisions exist on post-st-migration
fix_eol (dead) No revisions exist on post-st-migration
fix_annotations.pl (dead) No revisions exist on post-st-migration
find_subsys.pl (dead) No revisions exist on post-st-migration
find_special_proteins.pl (dead) No revisions exist on post-st-migration
find_selenoproteins.pl (dead) No revisions exist on post-st-migration
find_rnas.pl (dead) No revisions exist on post-st-migration
find_protein_homologs.pl (dead) No revisions exist on post-st-migration
find_poss_fs.pl (dead) No revisions exist on post-st-migration
find_poss_errs.pl (dead) No revisions exist on post-st-migration
find_new_annotations.pl (dead) No revisions exist on post-st-migration
find_neighbors_using_figfams.pl (dead) No revisions exist on post-st-migration
find_neighbors_by_sim.pl (dead) No revisions exist on post-st-migration
find_neighbors.pl (dead) No revisions exist on post-st-migration
find_more_instances_for_veronika.pl (dead) No revisions exist on post-st-migration
find_model_information_v2.pl (dead) No revisions exist on post-st-migration
find_model_information.pl (dead) No revisions exist on post-st-migration
find_model_cofactors.pl (dead) No revisions exist on post-st-migration
find_missing_lib_inputs_v2.pl (dead) No revisions exist on post-st-migration
find_missing_lib_inputs.pl (dead) No revisions exist on post-st-migration
find_missing_genes.pl (dead) No revisions exist on post-st-migration
find_miscalled_genes.pl (dead) No revisions exist on post-st-migration
find_maximal_clusters.pl (dead) No revisions exist on post-st-migration
find_genes_in_families.pl (dead) No revisions exist on post-st-migration
find_genes_based_on_neighbors_par.pl (dead) No revisions exist on post-st-migration
find_genes_based_on_neighbors.pl (dead) No revisions exist on post-st-migration
find_genes_based_on_kmers.pl (dead) No revisions exist on post-st-migration
find_gaps.pl (dead) No revisions exist on post-st-migration
find_essential_reactions.pl (dead) No revisions exist on post-st-migration
find_close_genomes.pl (dead) No revisions exist on post-st-migration
find_bidir_best_hits.pl (dead) No revisions exist on post-st-migration
find_bad_contigs.pl (dead) No revisions exist on post-st-migration
find_bad_conflicts.pl (dead) No revisions exist on post-st-migration
find_approx_neigh.pl (dead) No revisions exist on post-st-migration
find_SEED_SSU_rRNA_genes.pl (dead) No revisions exist on post-st-migration
find_RNA_genes.pl (dead) No revisions exist on post-st-migration
find_IS.pl (dead) No revisions exist on post-st-migration
filter_trunc_and_fs.pl (dead) No revisions exist on post-st-migration
filter_tbl_overlaps.pl (dead) No revisions exist on post-st-migration
filter_pegs_in_subsystems.pl (dead) No revisions exist on post-st-migration
filter_overlaps.pl (dead) No revisions exist on post-st-migration
filter_on_known.pl (dead) No revisions exist on post-st-migration
filter_new_overlaps.pl (dead) No revisions exist on post-st-migration
filter_figfams.pl (dead) No revisions exist on post-st-migration
filter_codon_counts.pl (dead) No revisions exist on post-st-migration
filter_and_merge_gene_sets.pl (dead) No revisions exist on post-st-migration
fill_subsys.pl (dead) No revisions exist on post-st-migration
fill_in_roles.pl (dead) No revisions exist on post-st-migration
fill_in_cell.pl (dead) No revisions exist on post-st-migration
figfam_subsystems.pl (dead) No revisions exist on post-st-migration
figfam_size_distribution.pl (dead) No revisions exist on post-st-migration
figfam_quality_control.pl (dead) No revisions exist on post-st-migration
figfam.pl (dead) No revisions exist on post-st-migration
fig_xmlrpc_server.pl (dead) No revisions exist on post-st-migration
fig_specific_sequences.pl (dead) No revisions exist on post-st-migration
fig_rpc.pl (dead) No revisions exist on post-st-migration
fig_net.pl (dead) No revisions exist on post-st-migration
fig_net (dead) No revisions exist on post-st-migration
fig.pl (dead) No revisions exist on post-st-migration
fig (dead) No revisions exist on post-st-migration
fid2dna.pl (dead) No revisions exist on post-st-migration
ff.pl (dead) No revisions exist on post-st-migration
fetch_seed_gto.pl (dead) No revisions exist on post-st-migration
fetch_models_for_genomes.pl (dead) No revisions exist on post-st-migration
features_with_role.pl (dead) No revisions exist on post-st-migration
feature_length_histogram.pl (dead) No revisions exist on post-st-migration
fc_figfams.pl (dead) No revisions exist on post-st-migration
fc.pl (dead) No revisions exist on post-st-migration
fastasize.c (dead) No revisions exist on post-st-migration
fasta_to_phylip.pl (dead) No revisions exist on post-st-migration
fasta_size.pl (dead) No revisions exist on post-st-migration
fasta_for_hypo.pl (dead) No revisions exist on post-st-migration
fasta_for_hypo (dead) No revisions exist on post-st-migration
fasta_dna.pl (dead) No revisions exist on post-st-migration
fasta_cksum.c (dead) No revisions exist on post-st-migration
fasta2phylip.pl (dead) No revisions exist on post-st-migration
fast_project_ref_to_GTO.pl (dead) No revisions exist on post-st-migration
fast_project.pl (dead) No revisions exist on post-st-migration
fast_grep.pl (dead) No revisions exist on post-st-migration
fast_blastp.pl (dead) No revisions exist on post-st-migration
fabric_vec.pl (dead) No revisions exist on post-st-migration
extract_subset_from_sprout_data.pl (dead) No revisions exist on post-st-migration
extract_sp_links.pl (dead) No revisions exist on post-st-migration
extract_metagene_contigs.pl (dead) No revisions exist on post-st-migration
extract_halo_genomes.pl (dead) No revisions exist on post-st-migration
extract_genomes_from_samples.pl (dead) No revisions exist on post-st-migration
extract_genomes.pl (dead) No revisions exist on post-st-migration
extract_genomes (dead) No revisions exist on post-st-migration
extract_genes.pl (dead) No revisions exist on post-st-migration
extract_fasta_idmap.pl (dead) No revisions exist on post-st-migration
extract_data_to_keep.pl (dead) No revisions exist on post-st-migration
extract_data_for_syncing_after_update.pl (dead) No revisions exist on post-st-migration
extract_DNA_sequence_from_object_for_start_predictions.pl (dead) No revisions exist on post-st-migration
extract_DNA_for_whole_ORFs.pl (dead) No revisions exist on post-st-migration
external_calls.pl (dead) No revisions exist on post-st-migration
extend_subsystem.pl (dead) No revisions exist on post-st-migration
extend_subsys.pl (dead) No revisions exist on post-st-migration
export_subsystem_as_gff.pl (dead) No revisions exist on post-st-migration
export_subsystem.pl (dead) No revisions exist on post-st-migration
export_similarity_request.pl (dead) No revisions exist on post-st-migration
export_phage_data.pl (dead) No revisions exist on post-st-migration
export_genome_as_gff.pl (dead) No revisions exist on post-st-migration
export_dlits.pl (dead) No revisions exist on post-st-migration
export_all_viruses.pl (dead) No revisions exist on post-st-migration
export_ACH_resolution_DB.pl (dead) No revisions exist on post-st-migration
explore_subsys_pmid.pl (dead) No revisions exist on post-st-migration
expand_transferred_chunks.pl (dead) No revisions exist on post-st-migration
expand_sims.pl (dead) No revisions exist on post-st-migration
expand_multifunctional_roles.pl (dead) No revisions exist on post-st-migration
expand_blast_table.pl (dead) No revisions exist on post-st-migration
expand_blast_table (dead) No revisions exist on post-st-migration
exp_pc_compute.pl (dead) No revisions exist on post-st-migration
exec-cgi.pl (dead) No revisions exist on post-st-migration
exclude_genomes.pl (dead) No revisions exist on post-st-migration
ex_split_atomic_regulons.pl (dead) No revisions exist on post-st-migration
ex_set_on_off_for_atomic_regulons.pl (dead) No revisions exist on post-st-migration
ex_rare_ar_and_pegs.pl (dead) No revisions exist on post-st-migration
ex_pipeline_ross.pl (dead) No revisions exist on post-st-migration
ex_make_on_off_calls.pl (dead) No revisions exist on post-st-migration
ex_make_initial_atomic_regulons.pl (dead) No revisions exist on post-st-migration
ex_get_subsystem_based_estimates.pl (dead) No revisions exist on post-st-migration
ex_get_adjacency_based_estimates.pl (dead) No revisions exist on post-st-migration
ex_fillout_ar_data.pl (dead) No revisions exist on post-st-migration
ex_compute_pccs.pl (dead) No revisions exist on post-st-migration
ex_adjust_peg_on_off.pl (dead) No revisions exist on post-st-migration
ex_add_conditions.pl (dead) No revisions exist on post-st-migration
evaluate_quality_of_trees.pl (dead) No revisions exist on post-st-migration
evaluate_properties.pl (dead) No revisions exist on post-st-migration
evaluate_annotation_consistency.pl (dead) No revisions exist on post-st-migration
eval_matrix.py (dead) No revisions exist on post-st-migration
ev_code_cron.pl (dead) No revisions exist on post-st-migration
estimated_fabric.pl (dead) No revisions exist on post-st-migration
ensure_genome_registration.pl (dead) No revisions exist on post-st-migration
embl2gff_addmd5.py (dead) No revisions exist on post-st-migration
embl2gff.pl (dead) No revisions exist on post-st-migration
ec_compare_sib.pl (dead) No revisions exist on post-st-migration
duplicate_genomes.pl (dead) No revisions exist on post-st-migration
dump_ss_classification.pl (dead) No revisions exist on post-st-migration
dump_machine_state.pl (dead) No revisions exist on post-st-migration
dump_attributes.pl (dead) No revisions exist on post-st-migration
dp.pl (dead) No revisions exist on post-st-migration
dose_response_sheets.pl (dead) No revisions exist on post-st-migration
dose_response_ic50.pl (dead) No revisions exist on post-st-migration
dose_response_extract.pl (dead) No revisions exist on post-st-migration
dna_seq.pl (dead) No revisions exist on post-st-migration
distribute_attributes.pl (dead) No revisions exist on post-st-migration
display_tree.pl (dead) No revisions exist on post-st-migration
direct_functional_coupling.pl (dead) No revisions exist on post-st-migration
difference_between_two_databases.pl (dead) No revisions exist on post-st-migration
diff_tbls.pl (dead) No revisions exist on post-st-migration
delete_genomes_from_sims.pl (dead) No revisions exist on post-st-migration
delete_genomes_from_sims (dead) No revisions exist on post-st-migration
delete_functions_for_nonextent_ff.pl (dead) No revisions exist on post-st-migration
delete_fids_from_orgdir.pl (dead) No revisions exist on post-st-migration
delete_all_attribute_files.pl (dead) No revisions exist on post-st-migration
db_xrefs_of.pl (dead) No revisions exist on post-st-migration
das_test.pl (dead) No revisions exist on post-st-migration
daily.pl (dead) No revisions exist on post-st-migration
curator_of.pl (dead) No revisions exist on post-st-migration
cs_adjacency_data.pl (dead) No revisions exist on post-st-migration
cripple_gto.pl (dead) No revisions exist on post-st-migration
create_sims_btree.pl (dead) No revisions exist on post-st-migration
create_partitions.pl (dead) No revisions exist on post-st-migration
create_ff_covering_skeleton.pl (dead) No revisions exist on post-st-migration
createTIGRfamSrc.pl (dead) No revisions exist on post-st-migration
create-new-page.pl (dead) No revisions exist on post-st-migration
crc64.py (dead) No revisions exist on post-st-migration
count_bases.pl (dead) No revisions exist on post-st-migration
correct_gff_missing_contigs.pl (dead) No revisions exist on post-st-migration
correct_frameshifts.pl (dead) No revisions exist on post-st-migration
corr_build_connections.pl (dead) No revisions exist on post-st-migration
core_PGF_stats.pl (dead) No revisions exist on post-st-migration
convert_tbl_files.pl (dead) No revisions exist on post-st-migration
convert-blast-to-m8.pl (dead) No revisions exist on post-st-migration
connections_between.pl (dead) No revisions exist on post-st-migration
connect_PDB_to_FIGfams_worker.pl (dead) No revisions exist on post-st-migration
connect_PDB_to_FIGfams.pl (dead) No revisions exist on post-st-migration
conditionally_assign.pl (dead) No revisions exist on post-st-migration
condense_kmer_output.pl (dead) No revisions exist on post-st-migration
condense_blast.pl (dead) No revisions exist on post-st-migration
condense_blast (dead) No revisions exist on post-st-migration
compute_translation_MD5.c (dead) No revisions exist on post-st-migration
compute_stats_for_kmer_hits.pl (dead) No revisions exist on post-st-migration
compute_simple_scores.pl (dead) No revisions exist on post-st-migration
compute_sim_chunk.pl (dead) No revisions exist on post-st-migration
compute_ribo_ratio_by_function.pl (dead) No revisions exist on post-st-migration
compute_ribo_ratio.pl (dead) No revisions exist on post-st-migration
compute_potential_fusions.pl (dead) No revisions exist on post-st-migration
compute_potential_fusions (dead) No revisions exist on post-st-migration
compute_pins_and_clusters.pl (dead) No revisions exist on post-st-migration
compute_pins.pl (dead) No revisions exist on post-st-migration
compute_pchs_from_sims.pl (dead) No revisions exist on post-st-migration
compute_pc.pl (dead) No revisions exist on post-st-migration
compute_new_ids.pl (dead) No revisions exist on post-st-migration
compute_mw_and_pi_with_BioPerl.pl (dead) No revisions exist on post-st-migration
compute_mw_and_pi.pl (dead) No revisions exist on post-st-migration
compute_genome_similarity.pl (dead) No revisions exist on post-st-migration
compute_genome_counts.pl (dead) No revisions exist on post-st-migration
compute_figfam_assignments.pl (dead) No revisions exist on post-st-migration
compute_fasta_lengths.pl (dead) No revisions exist on post-st-migration
compute_extra_dlit_data.pl (dead) No revisions exist on post-st-migration
compute_ev_code_attributes.pl (dead) No revisions exist on post-st-migration
compute_dbdir_checksum.pl (dead) No revisions exist on post-st-migration
compute_crc64_for_all_pegs.pl (dead) No revisions exist on post-st-migration
compute_contig_md5.pl (dead) No revisions exist on post-st-migration
compute_changed_ids_for_nrs.pl (dead) No revisions exist on post-st-migration
compute_changed_ids_for_nrs (dead) No revisions exist on post-st-migration
compute_atomic_regulons_for_dir.pl (dead) No revisions exist on post-st-migration
compute_atomic_regulons.pl (dead) No revisions exist on post-st-migration
compute_PSEED_reconstructions.pl (dead) No revisions exist on post-st-migration
compute_PCA_with_metagenomes_as_variables.pl (dead) No revisions exist on post-st-migration
compute_PCA_for_metagenomes.pl (dead) No revisions exist on post-st-migration
compute_CELLO_and_TMPRED.pl (dead) No revisions exist on post-st-migration
complete_genomes.pl (dead) No revisions exist on post-st-migration
complement_fasta.c (dead) No revisions exist on post-st-migration
compare_two_sets_of_calls.pl (dead) No revisions exist on post-st-migration
compare_tree_and_alignment.pl (dead) No revisions exist on post-st-migration
compare_tbls.pl (dead) No revisions exist on post-st-migration
compare_scenarios.pl (dead) No revisions exist on post-st-migration
compare_gto_called_CDSs.pl (dead) No revisions exist on post-st-migration
compare_gto_assigned_roles.pl (dead) No revisions exist on post-st-migration
compare_figfam_release_results.pl (dead) No revisions exist on post-st-migration
compare_ec_gary_table.pl (dead) No revisions exist on post-st-migration
compare_annotation_sets.pl (dead) No revisions exist on post-st-migration
compareMR.pl (dead) No revisions exist on post-st-migration
collect_related_sequences.pl (dead) No revisions exist on post-st-migration
collate_reads.pl (dead) No revisions exist on post-st-migration
codon_freq_eval_2.c (dead) No revisions exist on post-st-migration
codon_counts_x_and_p.c (dead) No revisions exist on post-st-migration
clustered_hypotheticals.pl (dead) No revisions exist on post-st-migration
cluster_objects.pl (dead) No revisions exist on post-st-migration
cluster_objects (dead) No revisions exist on post-st-migration
cluster_exp.pl (dead) No revisions exist on post-st-migration
cluster_by_sim.pl (dead) No revisions exist on post-st-migration
cluster_by_bbhs.pl (dead) No revisions exist on post-st-migration
clustal_to_fasta.pl (dead) No revisions exist on post-st-migration
clustal2fasta.pl (dead) No revisions exist on post-st-migration
close_connections.pl (dead) No revisions exist on post-st-migration
cleanup_figfams_updates.pl (dead) No revisions exist on post-st-migration
clean_subsystems.pl (dead) No revisions exist on post-st-migration
clean_sims.pl (dead) No revisions exist on post-st-migration
clean_sims (dead) No revisions exist on post-st-migration
clean_bad_contigs.pl (dead) No revisions exist on post-st-migration
check_tbl.pl (dead) No revisions exist on post-st-migration
check_tbl (dead) No revisions exist on post-st-migration
check_subsystems.pl (dead) No revisions exist on post-st-migration
check_subs_and_split_warnings.pl (dead) No revisions exist on post-st-migration
check_starts_for_pegs.pl (dead) No revisions exist on post-st-migration
check_starts_for_peg_sets.pl (dead) No revisions exist on post-st-migration
check_start_for_peg.pl (dead) No revisions exist on post-st-migration
check_sims_syntax.pl (dead) No revisions exist on post-st-migration
check_sims_for_added_genome.pl (dead) No revisions exist on post-st-migration
check_sims_basic.pl (dead) No revisions exist on post-st-migration
check_rast.pl (dead) No revisions exist on post-st-migration
check_peg_placement.pl (dead) No revisions exist on post-st-migration
check_peg_assignments.pl (dead) No revisions exist on post-st-migration
check_nr_and_peg_synonyms.pl (dead) No revisions exist on post-st-migration
check_model_v2.pl (dead) No revisions exist on post-st-migration
check_model.pl (dead) No revisions exist on post-st-migration
check_lost_sims.pl (dead) No revisions exist on post-st-migration
check_lost_sims (dead) No revisions exist on post-st-migration
check_hope_info.pl (dead) No revisions exist on post-st-migration
check_gto.pl (dead) No revisions exist on post-st-migration
check_genomes_by_ribo_proteins.pl (dead) No revisions exist on post-st-migration
check_for_unique_sims.pl (dead) No revisions exist on post-st-migration
check_for_unique_sims (dead) No revisions exist on post-st-migration
check_for_scenario_reachability.pl (dead) No revisions exist on post-st-migration
check_for_possible_mobile_elements.pl (dead) No revisions exist on post-st-migration
check_for_new_genomes.pl (dead) No revisions exist on post-st-migration
check_figfams.pl (dead) No revisions exist on post-st-migration
check_fasta_for_dups.pl (dead) No revisions exist on post-st-migration
check_fast_sims.pl (dead) No revisions exist on post-st-migration
check_fast_sims (dead) No revisions exist on post-st-migration
check_consistency_of_sample.pl (dead) No revisions exist on post-st-migration
check_consistency_of_rectangles.pl (dead) No revisions exist on post-st-migration
check_changes_in_organisms.pl (dead) No revisions exist on post-st-migration
check_changes_in_organisms (dead) No revisions exist on post-st-migration
check_and_extend_all_subsystems.pl (dead) No revisions exist on post-st-migration
check_all_subsystems.pl (dead) No revisions exist on post-st-migration
check_all_lost_sims.pl (dead) No revisions exist on post-st-migration
check_all_lost_sims (dead) No revisions exist on post-st-migration
check_alignment.pl (dead) No revisions exist on post-st-migration
changed_starts.pl (dead) No revisions exist on post-st-migration
cat_spreadsheet.pl (dead) No revisions exist on post-st-migration
cat_spreadsheet (dead) No revisions exist on post-st-migration
call_genome_using_glimmer.pl (dead) No revisions exist on post-st-migration
call_genes.pl (dead) No revisions exist on post-st-migration
call_coregulated_clusters_on_chromosome.pl (dead) No revisions exist on post-st-migration
cache_comparison_data.pl (dead) No revisions exist on post-st-migration
build_syn.pl (dead) No revisions exist on post-st-migration
build_solid_set.pl (dead) No revisions exist on post-st-migration
build_sets_from_clusters.pl (dead) No revisions exist on post-st-migration
build_sas_distro_from_cvs.pl (dead) No revisions exist on post-st-migration
build_sas_distro.pl (dead) No revisions exist on post-st-migration
build_sample_sigs.pl (dead) No revisions exist on post-st-migration
build_pssm_db.pl (dead) No revisions exist on post-st-migration
build_protein_families.pl (dead) No revisions exist on post-st-migration
build_prok_nonff_fasta.pl (dead) No revisions exist on post-st-migration
build_partition_index.pl (dead) No revisions exist on post-st-migration
build_nr_sources.pl (dead) No revisions exist on post-st-migration
build_nr_md5.pl (dead) No revisions exist on post-st-migration
build_nr.pl (dead) No revisions exist on post-st-migration
build_nr (dead) No revisions exist on post-st-migration
build_nohit_fasta.pl (dead) No revisions exist on post-st-migration
build_nohit_fasta (dead) No revisions exist on post-st-migration
build_new_figfam_release.pl (dead) No revisions exist on post-st-migration
build_nap_alignments.pl (dead) No revisions exist on post-st-migration
build_initial_objects_for_start_predictions.pl (dead) No revisions exist on post-st-migration
build_figfam_pssm_db.pl (dead) No revisions exist on post-st-migration
build_family_dir_from_genera.pl (dead) No revisions exist on post-st-migration
build_exemplar_fasta.pl (dead) No revisions exist on post-st-migration
build_exemplar_fasta (dead) No revisions exist on post-st-migration
build_excel_gene_table.pl (dead) No revisions exist on post-st-migration
build_excel_gene_table (dead) No revisions exist on post-st-migration
build_dtr_distro.pl (dead) No revisions exist on post-st-migration
build_dnaseq_blastdb.pl (dead) No revisions exist on post-st-migration
build_contigs_blastdb.pl (dead) No revisions exist on post-st-migration
build_anno_clearinghouse.pl (dead) No revisions exist on post-st-migration
build_all_prok_seqs.pl (dead) No revisions exist on post-st-migration
build_aligns_and_trees_for_seqs.pl (dead) No revisions exist on post-st-migration
build_alignments_from_spreadsheet.pl (dead) No revisions exist on post-st-migration
build_alignments_for_subsystems.pl (dead) No revisions exist on post-st-migration
build_access_sets.pl (dead) No revisions exist on post-st-migration
build_access_sets (dead) No revisions exist on post-st-migration
build_SEED_nr.pl (dead) No revisions exist on post-st-migration
build_PGs_for_OTUs.pl (dead) No revisions exist on post-st-migration
bring_tree_up_to_ali.pl (dead) No revisions exist on post-st-migration
bring_system_up_to_date.pl (dead) No revisions exist on post-st-migration
bring_system_up_to_date (dead) No revisions exist on post-st-migration
break_scaffolds.pl (dead) No revisions exist on post-st-migration
break_scaffolds (dead) No revisions exist on post-st-migration
br_evaluate_properties.pl (dead) No revisions exist on post-st-migration
boot_cluster_seed.pl (dead) No revisions exist on post-st-migration
blocked_by.pl (dead) No revisions exist on post-st-migration
blastp_pseq.pl (dead) No revisions exist on post-st-migration
blastp_pseq (dead) No revisions exist on post-st-migration
blastn_seqs.pl (dead) No revisions exist on post-st-migration
blastn_seqs (dead) No revisions exist on post-st-migration
blastn_chunks.pl (dead) No revisions exist on post-st-migration
blast_request.pl (dead) No revisions exist on post-st-migration
blast_request (dead) No revisions exist on post-st-migration
blast_pdb_against_nr_on_tla.pl (dead) No revisions exist on post-st-migration
blastP.pl (dead) No revisions exist on post-st-migration
blast2gff.pl (dead) No revisions exist on post-st-migration
bielefeld_tarfile_to_seed.pl (dead) No revisions exist on post-st-migration
best_tree_using_proml_on_cluster.pl (dead) No revisions exist on post-st-migration
best_hits.pl (dead) No revisions exist on post-st-migration
bbhs.pl (dead) No revisions exist on post-st-migration
bbh_synteny.pl (dead) No revisions exist on post-st-migration
bayes_expected_start_scores.pl (dead) No revisions exist on post-st-migration
batch_of_bbhs.pl (dead) No revisions exist on post-st-migration
backup_subsystems.pl (dead) No revisions exist on post-st-migration
backup_critical_data.pl (dead) No revisions exist on post-st-migration
backfill_gaps.pl (dead) No revisions exist on post-st-migration
auto_assign.pl (dead) No revisions exist on post-st-migration
auto_assign (dead) No revisions exist on post-st-migration
at.pl (dead) No revisions exist on post-st-migration
assigned_functions_from_rast.pl (dead) No revisions exist on post-st-migration
assign_with_no_sims.pl (dead) No revisions exist on post-st-migration
assign_with_no_sims (dead) No revisions exist on post-st-migration
assign_using_kmers.pl (dead) No revisions exist on post-st-migration
assign_using_ff_server_standalone.pl (dead) No revisions exist on post-st-migration
assign_using_ff_server_simple.pl (dead) No revisions exist on post-st-migration
assign_using_ff_server.pl (dead) No revisions exist on post-st-migration
assign_using_ff_parallel.pl (dead) No revisions exist on post-st-migration
assign_using_ff_original.pl (dead) No revisions exist on post-st-migration
assign_using_ff.pl (dead) No revisions exist on post-st-migration
assign_using_dna_server_standalone.pl (dead) No revisions exist on post-st-migration
assign_using_dna_server_simple.pl (dead) No revisions exist on post-st-migration
assign_using_dna_server.pl (dead) No revisions exist on post-st-migration
assign_towards_subsystems.pl (dead) No revisions exist on post-st-migration
assign_to_unchanged.pl (dead) No revisions exist on post-st-migration
assign_to_sets.pl (dead) No revisions exist on post-st-migration
assign_to_sets (dead) No revisions exist on post-st-migration
assign_to_hypo.pl (dead) No revisions exist on post-st-migration
assign_to_hypo (dead) No revisions exist on post-st-migration
assign_to_dna_using_kmers.pl (dead) No revisions exist on post-st-migration
assign_to_close_strains.pl (dead) No revisions exist on post-st-migration
assign_synonym_ids_to_sims.pl (dead) No revisions exist on post-st-migration
assign_synonym_ids_to_nr.pl (dead) No revisions exist on post-st-migration
assign_synonym_ids.pl (dead) No revisions exist on post-st-migration
assign_figfam.pl (dead) No revisions exist on post-st-migration
assign.pl (dead) No revisions exist on post-st-migration
assign (dead) No revisions exist on post-st-migration
assess_quality.pl (dead) No revisions exist on post-st-migration
assess_genome_quality.pl (dead) No revisions exist on post-st-migration
assess_gene_call_quality.pl (dead) No revisions exist on post-st-migration
assess_completeness.pl (dead) No revisions exist on post-st-migration
assemble_selected.pl (dead) No revisions exist on post-st-migration
are_close.pl (dead) No revisions exist on post-st-migration
apply_peg_changes_to_subsystem.pl (dead) No revisions exist on post-st-migration
apply_map.pl (dead) No revisions exist on post-st-migration
apply_map (dead) No revisions exist on post-st-migration
apply_automatic_subsystem_updates.pl (dead) No revisions exist on post-st-migration
apply_annotations.pl (dead) No revisions exist on post-st-migration
annotation_counts.pl (dead) No revisions exist on post-st-migration
annotate-ss-with-pattyfams.pl (dead) No revisions exist on post-st-migration
analyze_scenario_connections.pl (dead) No revisions exist on post-st-migration
analyze_package_logs.pl (dead) No revisions exist on post-st-migration
analyze_loose_sets.pl (dead) No revisions exist on post-st-migration
analyze_kmer_assignments.pl (dead) No revisions exist on post-st-migration
alter_tbl.pl (dead) No revisions exist on post-st-migration
all_subsystems.pl (dead) No revisions exist on post-st-migration
all_bbhs.pl (dead) No revisions exist on post-st-migration
alignment_to_html.pl (dead) No revisions exist on post-st-migration
align_with_clustal_2.pl (dead) No revisions exist on post-st-migration
align_with_clustal.pl (dead) No revisions exist on post-st-migration
align_with_clustal (dead) No revisions exist on post-st-migration
align_seqs.pl (dead) No revisions exist on post-st-migration
align_fasta.pl (dead) No revisions exist on post-st-migration
aliases_of.pl (dead) No revisions exist on post-st-migration
alias2fig.pl (dead) No revisions exist on post-st-migration
ali_tree.pl (dead) No revisions exist on post-st-migration
ali_to_seq.pl (dead) No revisions exist on post-st-migration
adjacent.pl (dead) No revisions exist on post-st-migration
add_to_subsystems.pl (dead) No revisions exist on post-st-migration
add_to_alignment.pl (dead) No revisions exist on post-st-migration
add_structured_english.pl (dead) No revisions exist on post-st-migration
add_start_data_for_start_predictions.pl (dead) No revisions exist on post-st-migration
add_sim_data_for_start_predictions.pl (dead) No revisions exist on post-st-migration
add_rbs_data_for_start_predictions.pl (dead) No revisions exist on post-st-migration
add_prots_to_tree.pl (dead) No revisions exist on post-st-migration
add_phage_from_rast.sh (dead) No revisions exist on post-st-migration
add_figbar_and_genome_attributes.pl (dead) No revisions exist on post-st-migration
add_dlits.pl (dead) No revisions exist on post-st-migration
add_close_genes.pl (dead) No revisions exist on post-st-migration
add_attributes_from_file.pl (dead) No revisions exist on post-st-migration
add_assignments.pl (dead) No revisions exist on post-st-migration
add_assertions_of_function.pl (dead) No revisions exist on post-st-migration
add_assertions_of_function (dead) No revisions exist on post-st-migration
aclh_reload_contrib.pl (dead) No revisions exist on post-st-migration
aclh.pl (dead) No revisions exist on post-st-migration
accumulate_pegs_to_scenario_paths.pl (dead) No revisions exist on post-st-migration
WikiMaker.pl (dead) No revisions exist on post-st-migration
WebAppBackend.pl (dead) No revisions exist on post-st-migration
TransactFeatures.pl (dead) No revisions exist on post-st-migration
Tracer.pl (dead) No revisions exist on post-st-migration
TestLocations.pl (dead) No revisions exist on post-st-migration
SwissProtXML_to_JSON.pl (dead) No revisions exist on post-st-migration
SwissProtJSON_to_loadfile.pl (dead) No revisions exist on post-st-migration
SplitGeneSets.R (dead) No revisions exist on post-st-migration
SpanishInquisition.pl (dead) No revisions exist on post-st-migration
Simple.pl (dead) No revisions exist on post-st-migration
ShewanellaRMA.R (dead) No revisions exist on post-st-migration
SStest.pl (dead) No revisions exist on post-st-migration
RunRMA_SIF_format.R (dead) No revisions exist on post-st-migration
RunRMA.R (dead) No revisions exist on post-st-migration
README (dead) No revisions exist on post-st-migration
Pipeline.R (dead) No revisions exist on post-st-migration
PickGeneBoundariesTest.pl (dead) No revisions exist on post-st-migration
Packager.pl (dead) No revisions exist on post-st-migration
OneShotAttributeAdder.pl (dead) No revisions exist on post-st-migration
NMPDRAnalysis.pl (dead) No revisions exist on post-st-migration
ModelDriver.pl (dead) No revisions exist on post-st-migration
Makefile.cprogs (dead) No revisions exist on post-st-migration
Makefile (dead) No revisions exist on post-st-migration
MFADriver.pl (dead) No revisions exist on post-st-migration
ListLits.pl (dead) No revisions exist on post-st-migration
LigandCleanup.pl (dead) No revisions exist on post-st-migration
KeyDump.pl (dead) No revisions exist on post-st-migration
GenomeTypeObject.t (dead) No revisions exist on post-st-migration
GeneSet_P_Values.R (dead) No revisions exist on post-st-migration
GTO_to_PGF_genome_stats.pl (dead) No revisions exist on post-st-migration
FIGMODELscheduler.pl (dead) No revisions exist on post-st-migration
FFB3_usable_motifs.pl (dead) No revisions exist on post-st-migration
FFB3_update_FIGfams.pl (dead) No revisions exist on post-st-migration
FFB3_set_figfam_functions.pl (dead) No revisions exist on post-st-migration
FFB3_run_tests.pl (dead) No revisions exist on post-st-migration
FFB3_run_parallel_usable_motifs.pl (dead) No revisions exist on post-st-migration
FFB3_package_figfams.pl (dead) No revisions exist on post-st-migration
FFB3_merge_families_by_kmers.pl (dead) No revisions exist on post-st-migration
FFB3_merge_and_build_kmers.pl (dead) No revisions exist on post-st-migration
FFB3_make_subsys_based_families_2.pl (dead) No revisions exist on post-st-migration
FFB3_make_subsys_based_families.pl (dead) No revisions exist on post-st-migration
FFB3_load_oligo_index.pl (dead) No revisions exist on post-st-migration
FFB3_get_recent_annotations.pl (dead) No revisions exist on post-st-migration
FFB3_get_oligos.pl (dead) No revisions exist on post-st-migration
FFB3_get_gs_oligos.pl (dead) No revisions exist on post-st-migration
FFB3_families_to_fasta.pl (dead) No revisions exist on post-st-migration
FFB3_create_binary_kmers.pl (dead) No revisions exist on post-st-migration
FFB3_construct_assigned_functions.pl (dead) No revisions exist on post-st-migration
FFB3_compare_tests.pl (dead) No revisions exist on post-st-migration
FFB3_cleanup_families.pl (dead) No revisions exist on post-st-migration
FFB3_build_updated_FF.pl (dead) No revisions exist on post-st-migration
FFB3_build_otu_oligos.pl (dead) No revisions exist on post-st-migration
FFB3_build_ff_oligos.pl (dead) No revisions exist on post-st-migration
FFB3_build_ff_indexes.pl (dead) No revisions exist on post-st-migration
FFB3_assemble_translations.pl (dead) No revisions exist on post-st-migration
FFB2_xy.pl (dead) No revisions exist on post-st-migration
FFB2_xx.pl (dead) No revisions exist on post-st-migration
FFB2_validate_families.pl (dead) No revisions exist on post-st-migration
FFB2_usable_motifs2.pl (dead) No revisions exist on post-st-migration
FFB2_usable_motifs.pl (dead) No revisions exist on post-st-migration
FFB2_update_FIGfams.pl (dead) No revisions exist on post-st-migration
FFB2_split_fams_by_size.pl (dead) No revisions exist on post-st-migration
FFB2_run_tests.pl (dead) No revisions exist on post-st-migration
FFB2_pull_extreme_FF_members.pl (dead) No revisions exist on post-st-migration
FFB2_merge_oligos.pl (dead) No revisions exist on post-st-migration
FFB2_merge_families_based_on_genus_groups.pl (dead) No revisions exist on post-st-migration
FFB2_merge_and_build_kmers.pl (dead) No revisions exist on post-st-migration
FFB2_make_subsys_based_families.pl (dead) No revisions exist on post-st-migration
FFB2_make_family_vector.pl (dead) No revisions exist on post-st-migration
FFB2_make_FF_index.pl (dead) No revisions exist on post-st-migration
FFB2_load_oligo_index.pl (dead) No revisions exist on post-st-migration
FFB2_load_memcache.pl (dead) No revisions exist on post-st-migration
FFB2_install_kmers.pl (dead) No revisions exist on post-st-migration
FFB2_get_prots.pl (dead) No revisions exist on post-st-migration
FFB2_get_prot_gs_oligos.pl (dead) No revisions exist on post-st-migration
FFB2_get_oligos2.pl (dead) No revisions exist on post-st-migration
FFB2_get_oligos.pl (dead) No revisions exist on post-st-migration
FFB2_genome_group_pipeline.pl (dead) No revisions exist on post-st-migration
FFB2_families_in_subsystems.pl (dead) No revisions exist on post-st-migration
FFB2_create_binary_relationships.pl (dead) No revisions exist on post-st-migration
FFB2_create_binary_kmers.pl (dead) No revisions exist on post-st-migration
FFB2_compute_relationships_for_genera.pl (dead) No revisions exist on post-st-migration
FFB2_compare_to_anno3.pl (dead) No revisions exist on post-st-migration
FFB2_compare_tests.pl (dead) No revisions exist on post-st-migration
FFB2_build_updated_FF.pl (dead) No revisions exist on post-st-migration
FFB2_build_ff_indexes.pl (dead) No revisions exist on post-st-migration
EmergencySubsystemFix.pl (dead) No revisions exist on post-st-migration
EmergencyMapFlipper.pl (dead) No revisions exist on post-st-migration
EcoliRMA.R (dead) No revisions exist on post-st-migration
Consistency_Families.pm (dead) No revisions exist on post-st-migration
ComputeSproutSequences.pl (dead) No revisions exist on post-st-migration
ComputeSproutCouplings.pl (dead) No revisions exist on post-st-migration
CheckCELfiles.R (dead) No revisions exist on post-st-migration
CS_compute_coupling.pl (dead) No revisions exist on post-st-migration
CS_build_fasta_for_phylogeny.pl (dead) No revisions exist on post-st-migration
CSA_second_pass.pl (dead) No revisions exist on post-st-migration
CSA_ref_vs_ref.pl (dead) No revisions exist on post-st-migration
CSA_predict_features_based_on_refs.pl (dead) No revisions exist on post-st-migration
CSA_merge_estimates.pl (dead) No revisions exist on post-st-migration
CSA_make_unique_kmers.pl (dead) No revisions exist on post-st-migration
CSA_make_contig_index.pl (dead) No revisions exist on post-st-migration
CSA_make_conn.pl (dead) No revisions exist on post-st-migration
CSA_layout.pl (dead) No revisions exist on post-st-migration
CSA_get_repeat_dna.pl (dead) No revisions exist on post-st-migration
CSA_get_close_strain_annotations.pl (dead) No revisions exist on post-st-migration
CSA_gather_mapped_objects.pl (dead) No revisions exist on post-st-migration
CSA_first_pass.pl (dead) No revisions exist on post-st-migration
CSA_filter_unique.pl (dead) No revisions exist on post-st-migration
CSA_create_SNP_data.pl (dead) No revisions exist on post-st-migration
CSA_collapse_repeats.pl (dead) No revisions exist on post-st-migration
CSA_close_strains.pl (dead) No revisions exist on post-st-migration
CSA_build_alignments.pl (dead) No revisions exist on post-st-migration
COPYING.TXT (dead) No revisions exist on post-st-migration
BuildCodonUsageExchAndLoadFiles.pl (dead) No revisions exist on post-st-migration

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