Hotspots_Paper_2024

Scripts used in 2024 Hotspots paper

The scripts are Python or Unix and provided as last used in performing analyses for the Hotspots paper. Inputs and outputs for individual scripts will need filepaths updated to local directory structure. Conda or other installations of the following are assumed to be activated:

Blast suite

OrthoFinder2

InterProScan5

Mafft7

Clipkit

FastTree2

BUSCO5

Details on genomes and their associated GTF/GFF files are provided in the paper in Supplemental Table 1. Pre-processed longest protein per gene (T1) proteomes used in the script pipelines are also provided in the paper as supplemental materials.

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Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
README.md		README.md
blast-001-blastp-self_X_self		blast-001-blastp-self_X_self
blast-002-blastp-species_X_genetic_models		blast-002-blastp-species_X_genetic_models
blast-003-list-genetic-model-blast-reports		blast-003-list-genetic-model-blast-reports
blast-004-python-blast-genetic-models-dark-matter		blast-004-python-blast-genetic-models-dark-matter
busco-001-ls-fastas		busco-001-ls-fastas
busco-002-python-code-busco-all-genomes---USER_INPUT		busco-002-python-code-busco-all-genomes---USER_INPUT
busco-003-busco-T1-proteomes		busco-003-busco-T1-proteomes
busco-004-cat-short-summaries		busco-004-cat-short-summaries
busco-005-busco-genomes		busco-005-busco-genomes
darkmatter-007-python-calculate-genomic-dark-matter-for-species16		darkmatter-007-python-calculate-genomic-dark-matter-for-species16
domains-000-setup		domains-000-setup
domains-001-ls-fastas		domains-001-ls-fastas
domains-002-python-interproscan-ALL		domains-002-python-interproscan-ALL
domains-003-interproscan-all-apps-all-species		domains-003-interproscan-all-apps-all-species
domains-004-ls-interproscan-tsvs		domains-004-ls-interproscan-tsvs
domains-005-python-interproscan-parser		domains-005-python-interproscan-parser
domains-006-ls-interproscan-parsed		domains-006-ls-interproscan-parsed
domains-007-python-interproscan-annotation-counter		domains-007-python-interproscan-annotation-counter
domains-008-python-tool-annotations-per-sequence-across-species		domains-008-python-tool-annotations-per-sequence-across-species
domains-009-ls-parsed-interproscan-files		domains-009-ls-parsed-interproscan-files
domains-010-python-add-in-sequences-with-no-interproscan-annotation		domains-010-python-add-in-sequences-with-no-interproscan-annotation
domains-011-ls-files-to-keep-as-output-and-update-to-source-ids		domains-011-ls-files-to-keep-as-output-and-update-to-source-ids
domains-012-python-sourceids		domains-012-python-sourceids
domains-013-interproscan-genomic-dark-matter-counts		domains-013-interproscan-genomic-dark-matter-counts
gigantic_homologs-000-setup		gigantic_homologs-000-setup
gigantic_homologs-001-ls-blastdbs		gigantic_homologs-001-ls-blastdbs
gigantic_homologs-002-python-command-blastp		gigantic_homologs-002-python-command-blastp
gigantic_homologs-003-blastp_X_projectDB		gigantic_homologs-003-blastp_X_projectDB
gigantic_homologs-004-ls-reports-and-fastas		gigantic_homologs-004-ls-reports-and-fastas
gigantic_homologs-005-python-gene-set-fasta		gigantic_homologs-005-python-gene-set-fasta
gigantic_homologs-006-blastp-rgs_X_rgs-genomes		gigantic_homologs-006-blastp-rgs_X_rgs-genomes
gigantic_homologs-007-ls-rgs-reports-fastas		gigantic_homologs-007-ls-rgs-reports-fastas
gigantic_homologs-008-python-update-reference-genomes		gigantic_homologs-008-python-update-reference-genomes
gigantic_homologs-009-ls-reference-genome-fastas		gigantic_homologs-009-ls-reference-genome-fastas
gigantic_homologs-010-python-command-makeblastdb		gigantic_homologs-010-python-command-makeblastdb
gigantic_homologs-011-blastp-makedb		gigantic_homologs-011-blastp-makedb
gigantic_homologs-012-ls-blastp-rgs-genomes		gigantic_homologs-012-ls-blastp-rgs-genomes
gigantic_homologs-013-python-command-blastp		gigantic_homologs-013-python-command-blastp
gigantic_homologs-014-blastp-hits_X_RGS-genomes		gigantic_homologs-014-blastp-hits_X_RGS-genomes
gigantic_homologs-015-cat-all-blastp-reports		gigantic_homologs-015-cat-all-blastp-reports
gigantic_homologs-016-python-RBF-CGS-each-RGS-genome-fasta		gigantic_homologs-016-python-RBF-CGS-each-RGS-genome-fasta
gigantic_homologs-017-cat-RGS-CGS-fasta		gigantic_homologs-017-cat-RGS-CGS-fasta
gigantic_homologs-018-python-TRPs-per-species.py		gigantic_homologs-018-python-TRPs-per-species.py
gigantic_homologs-019-cat-species-subsets		gigantic_homologs-019-cat-species-subsets
gigantic_trees-000-setup		gigantic_trees-000-setup
gigantic_trees-001-sed-dashes-for-mafft		gigantic_trees-001-sed-dashes-for-mafft
gigantic_trees-002-sed-U		gigantic_trees-002-sed-U
gigantic_trees-003-mafft		gigantic_trees-003-mafft
gigantic_trees-004-clipkit-smartgap		gigantic_trees-004-clipkit-smartgap
gigantic_trees-006-fasttree		gigantic_trees-006-fasttree
hotspots-001-ls-blast-reports-gtfs		hotspots-001-ls-blast-reports-gtfs
hotspots-002-python-parse-blast-reports-for-within-species-homologs.py		hotspots-002-python-parse-blast-reports-for-within-species-homologs.py
hotspots-003-python-identify-hotspots.py		hotspots-003-python-identify-hotspots.py
hotspots-004-ls-trees		hotspots-004-ls-trees
hotspots-005-python-integrate-gigantic-orthogroup-trees-with-paralog-hotspots		hotspots-005-python-integrate-gigantic-orthogroup-trees-with-paralog-hotspots
hotspots-006-python-count-hotspots-per-species		hotspots-006-python-count-hotspots-per-species
hotspots-007-python-trps-hotspots-stats		hotspots-007-python-trps-hotspots-stats
orthogroups-001-orthofinder-hotspots		orthogroups-001-orthofinder-hotspots
orthogroups-002-list-gigantic-fastas		orthogroups-002-list-gigantic-fastas
orthogroups-003-python-integrate-gigantic_X_orthofinder		orthogroups-003-python-integrate-gigantic_X_orthofinder
orthogroups-004-ls-fastas		orthogroups-004-ls-fastas
orthogroups-005-python-orthofinder-dark-matters		orthogroups-005-python-orthofinder-dark-matters

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