├── .github └── workflows │ ├── test-conda-installs.yml │ └── test-full-run.yml ├── .gitignore ├── CHANGELOG.md ├── LICENSE ├── README.md ├── bin ├── GToTree ├── gtt-align-and-trim-parallel.sh ├── gtt-amino-acid-parallel.sh ├── gtt-amino-acid-serial.sh ├── gtt-append-fasta-headers ├── gtt-cat-alignments ├── gtt-check-or-setup-GTDB-files ├── gtt-check-wanted-lineage-info ├── gtt-clean-after-test.sh ├── gtt-combine-kofamscan-results.sh ├── gtt-count-bases-per-seq ├── gtt-data-locations ├── gtt-fasta-parallel-nt.sh ├── gtt-fasta-parallel.sh ├── gtt-fasta-serial-nt.sh ├── gtt-fasta-serial.sh ├── gtt-filter-parallel.sh ├── gtt-filter-seqs-by-length ├── gtt-gen-KO-iToL-files.sh ├── gtt-gen-SCG-HMMs ├── gtt-gen-itol-map ├── gtt-gen-pfam-iToL-files.sh ├── gtt-genbank-parallel.sh ├── gtt-genbank-serial.sh ├── gtt-genbank-to-AA-seqs ├── gtt-genbank-to-fasta ├── gtt-get-accessions-from-GTDB ├── gtt-get-additional-pfam-targets.sh ├── gtt-get-kofamscan-data ├── gtt-get-median.sh ├── gtt-get-ncbi-assembly-tables ├── gtt-get-ncbi-tax-data ├── gtt-hmms ├── gtt-ncbi-parallel-nt.sh ├── gtt-ncbi-parallel.sh ├── gtt-ncbi-serial-nt.sh ├── gtt-ncbi-serial.sh ├── gtt-parse-assembly-summary-file ├── gtt-parse-fasta-by-headers ├── gtt-parse-gtdb-assembly-summary-file ├── gtt-parse-kofamscan-targets.sh ├── gtt-pfam-search ├── gtt-remove-all-gap-seqs-from-alignment ├── gtt-rename-fasta-headers ├── gtt-reorder-fasta ├── gtt-run-additional-pfam-search.sh ├── gtt-run-kofamscan.sh ├── gtt-store-SCG-HMMs ├── gtt-subset-GTDB-accessions ├── gtt-swap-ids ├── gtt-test.sh └── gtt-update-ncbi-taxonomy └── hmm_sets └── hmm-sources-and-info.tsv /.github/workflows/test-conda-installs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/.github/workflows/test-conda-installs.yml -------------------------------------------------------------------------------- /.github/workflows/test-full-run.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/.github/workflows/test-full-run.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | notes.txt 3 | GToTree.egg-info/ 4 | build/ 5 | gtotree/ 6 | -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/README.md -------------------------------------------------------------------------------- /bin/GToTree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/GToTree -------------------------------------------------------------------------------- /bin/gtt-align-and-trim-parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-align-and-trim-parallel.sh -------------------------------------------------------------------------------- /bin/gtt-amino-acid-parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-amino-acid-parallel.sh -------------------------------------------------------------------------------- /bin/gtt-amino-acid-serial.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-amino-acid-serial.sh -------------------------------------------------------------------------------- /bin/gtt-append-fasta-headers: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-append-fasta-headers -------------------------------------------------------------------------------- /bin/gtt-cat-alignments: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-cat-alignments -------------------------------------------------------------------------------- /bin/gtt-check-or-setup-GTDB-files: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-check-or-setup-GTDB-files -------------------------------------------------------------------------------- /bin/gtt-check-wanted-lineage-info: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-check-wanted-lineage-info -------------------------------------------------------------------------------- /bin/gtt-clean-after-test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-clean-after-test.sh -------------------------------------------------------------------------------- /bin/gtt-combine-kofamscan-results.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-combine-kofamscan-results.sh -------------------------------------------------------------------------------- /bin/gtt-count-bases-per-seq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-count-bases-per-seq -------------------------------------------------------------------------------- /bin/gtt-data-locations: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-data-locations -------------------------------------------------------------------------------- /bin/gtt-fasta-parallel-nt.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-fasta-parallel-nt.sh -------------------------------------------------------------------------------- /bin/gtt-fasta-parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-fasta-parallel.sh -------------------------------------------------------------------------------- /bin/gtt-fasta-serial-nt.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-fasta-serial-nt.sh -------------------------------------------------------------------------------- /bin/gtt-fasta-serial.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-fasta-serial.sh -------------------------------------------------------------------------------- /bin/gtt-filter-parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-filter-parallel.sh -------------------------------------------------------------------------------- /bin/gtt-filter-seqs-by-length: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-filter-seqs-by-length -------------------------------------------------------------------------------- /bin/gtt-gen-KO-iToL-files.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-gen-KO-iToL-files.sh -------------------------------------------------------------------------------- /bin/gtt-gen-SCG-HMMs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-gen-SCG-HMMs -------------------------------------------------------------------------------- /bin/gtt-gen-itol-map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-gen-itol-map -------------------------------------------------------------------------------- /bin/gtt-gen-pfam-iToL-files.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-gen-pfam-iToL-files.sh -------------------------------------------------------------------------------- /bin/gtt-genbank-parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-genbank-parallel.sh -------------------------------------------------------------------------------- /bin/gtt-genbank-serial.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-genbank-serial.sh -------------------------------------------------------------------------------- /bin/gtt-genbank-to-AA-seqs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-genbank-to-AA-seqs -------------------------------------------------------------------------------- /bin/gtt-genbank-to-fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-genbank-to-fasta -------------------------------------------------------------------------------- /bin/gtt-get-accessions-from-GTDB: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-get-accessions-from-GTDB -------------------------------------------------------------------------------- /bin/gtt-get-additional-pfam-targets.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-get-additional-pfam-targets.sh -------------------------------------------------------------------------------- /bin/gtt-get-kofamscan-data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-get-kofamscan-data -------------------------------------------------------------------------------- /bin/gtt-get-median.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-get-median.sh -------------------------------------------------------------------------------- /bin/gtt-get-ncbi-assembly-tables: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-get-ncbi-assembly-tables -------------------------------------------------------------------------------- /bin/gtt-get-ncbi-tax-data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-get-ncbi-tax-data -------------------------------------------------------------------------------- /bin/gtt-hmms: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-hmms -------------------------------------------------------------------------------- /bin/gtt-ncbi-parallel-nt.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-ncbi-parallel-nt.sh -------------------------------------------------------------------------------- /bin/gtt-ncbi-parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-ncbi-parallel.sh -------------------------------------------------------------------------------- /bin/gtt-ncbi-serial-nt.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-ncbi-serial-nt.sh -------------------------------------------------------------------------------- /bin/gtt-ncbi-serial.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-ncbi-serial.sh -------------------------------------------------------------------------------- /bin/gtt-parse-assembly-summary-file: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-parse-assembly-summary-file -------------------------------------------------------------------------------- /bin/gtt-parse-fasta-by-headers: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-parse-fasta-by-headers -------------------------------------------------------------------------------- /bin/gtt-parse-gtdb-assembly-summary-file: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-parse-gtdb-assembly-summary-file -------------------------------------------------------------------------------- /bin/gtt-parse-kofamscan-targets.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-parse-kofamscan-targets.sh -------------------------------------------------------------------------------- /bin/gtt-pfam-search: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-pfam-search -------------------------------------------------------------------------------- /bin/gtt-remove-all-gap-seqs-from-alignment: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-remove-all-gap-seqs-from-alignment -------------------------------------------------------------------------------- /bin/gtt-rename-fasta-headers: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-rename-fasta-headers -------------------------------------------------------------------------------- /bin/gtt-reorder-fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-reorder-fasta -------------------------------------------------------------------------------- /bin/gtt-run-additional-pfam-search.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-run-additional-pfam-search.sh -------------------------------------------------------------------------------- /bin/gtt-run-kofamscan.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-run-kofamscan.sh -------------------------------------------------------------------------------- /bin/gtt-store-SCG-HMMs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-store-SCG-HMMs -------------------------------------------------------------------------------- /bin/gtt-subset-GTDB-accessions: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-subset-GTDB-accessions -------------------------------------------------------------------------------- /bin/gtt-swap-ids: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-swap-ids -------------------------------------------------------------------------------- /bin/gtt-test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-test.sh -------------------------------------------------------------------------------- /bin/gtt-update-ncbi-taxonomy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/bin/gtt-update-ncbi-taxonomy -------------------------------------------------------------------------------- /hmm_sets/hmm-sources-and-info.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AstrobioMike/GToTree/HEAD/hmm_sets/hmm-sources-and-info.tsv --------------------------------------------------------------------------------