{"id":17844819,"url":"https://github.com/dombennett/pg-lt","last_synced_at":"2026-01-21T15:32:58.710Z","repository":{"id":10363270,"uuid":"12504034","full_name":"DomBennett/pG-lt","owner":"DomBennett","description":":pig::evergreen_tree: Pipeline for the automated generation of phylogenies from lists of taxon 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pG-lt\n[![Build Status](https://travis-ci.org/DomBennett/pG-lt.svg)](https://travis-ci.org/DomBennett/pG-lt)\n[![Coverage Status](https://coveralls.io/repos/DomBennett/pG-lt/badge.svg?branch=master)](https://coveralls.io/r/DomBennett/pG-lt?branch=master)\n\n'[phyloGenerator][pG]-light' or `pG-lt` is a python package for the automated\ngeneration of phylogenies from multiple lists of taxon names.\n\nThe package implements a pipeline that uses 'mass phylogeny estimation' to\ngenerate distributions of phylogenies from multiple sequences and alignments\nwith minimum human-input.\n\nThe pipeline consists of four stages: names resolution, sequence download,\nsequence alignment and phylogeny estimation.\n\npG-lt is a member of the phyloGenerator family.\n\n## Installation and usage\n\nAvailable on pip: `pip install pglt`.\n\nSet dependencies: `pglt_set_dependencies.py`\n\nRun: `run_pglt.py -e [EMAIL ADDRESS]`\n\nSee [wiki][wiki] for further information on how to use and install.\n\n## Features\n\n* One-line implementation: `run_pglt.py -e [EMAIL ADDRESS]`\n* Automatic or user specified parameters\n* Fuzzy taxonomic name matching\n* Automatic outgroup selection\n* Heuristic gene selection\n* Automatic sequence download with taxonomic context\n* Heuristic alignment and phylogeny checking\n* Rate partitioning between genes and codon positions\n* HPC compatible\n* Runs on Windows, OSX and Linux\n\n## External dependencies\n\n* Alignment tools: [MAFFT][mafft] and stand-alone [BLAST][blast]\n* Phylogeny tools: [RAxML][raxml]\n\n## Version\n\n*pG-lt is still in its developmental stage.*\n\n## License\n\nGPL v.2\n\n## Authors\n[Dom Bennett][db], [Will Pearse][wp], [Lawrence Hudson][lh],\n[Gerard Gorman][gg] and [Andy Purvis][ap]\n\n\u003c!-- References --\u003e\n[db]: https://github.com/DomBennett\n[wp]: https://github.com/willpearse\n[lh]: https://github.com/quicklizard99\n[gg]: https://github.com/ggorman\n[ap]: https://github.com/AndyPurvis\n[pG]: http://willpearse.github.io/phyloGenerator/\n[wiki]: https://github.com/DomBennett/pG-lt/wiki\n[mafft]: http://mafft.cbrc.jp/alignment/software/\n[raxml]: https://github.com/stamatak/standard-RAxML\n[blast]: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs\u0026DOC_TYPE=Download\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fpg-lt","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdombennett%2Fpg-lt","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fpg-lt/lists"}