https://github.com/dombennett/pg-lt

:pig::evergreen_tree: Pipeline for the automated generation of phylogenies from lists of taxon names
https://github.com/dombennett/pg-lt

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:pig::evergreen_tree: Pipeline for the automated generation of phylogenies from lists of taxon names

• Host: GitHub
• URL: https://github.com/dombennett/pg-lt
• Owner: DomBennett
• License: gpl-2.0
• Created: 2013-08-31T10:30:01.000Z (about 11 years ago)
• Default Branch: master
• Last Pushed: 2016-01-05T17:38:40.000Z (almost 9 years ago)
• Last Synced: 2024-09-23T05:42:16.844Z (about 1 month ago)
• Language: Python
• Homepage: https://github.com/DomBennett/pG-lt/wiki
• Size: 3.18 MB
• Stars: 3
• Watchers: 3
• Forks: 1
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

        
# pG-lt

[![Build Status](https://travis-ci.org/DomBennett/pG-lt.svg)](https://travis-ci.org/DomBennett/pG-lt)

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'[phyloGenerator][pG]-light' or `pG-lt` is a python package for the automated

generation of phylogenies from multiple lists of taxon names.

The package implements a pipeline that uses 'mass phylogeny estimation' to

generate distributions of phylogenies from multiple sequences and alignments

with minimum human-input.

The pipeline consists of four stages: names resolution, sequence download,

sequence alignment and phylogeny estimation.

pG-lt is a member of the phyloGenerator family.

## Installation and usage

Available on pip: `pip install pglt`.

Set dependencies: `pglt_set_dependencies.py`

Run: `run_pglt.py -e [EMAIL ADDRESS]`

See [wiki][wiki] for further information on how to use and install.

## Features

* One-line implementation: `run_pglt.py -e [EMAIL ADDRESS]`

* Automatic or user specified parameters

* Fuzzy taxonomic name matching

* Automatic outgroup selection

* Heuristic gene selection

* Automatic sequence download with taxonomic context

* Heuristic alignment and phylogeny checking

* Rate partitioning between genes and codon positions

* HPC compatible

* Runs on Windows, OSX and Linux

## External dependencies

* Alignment tools: [MAFFT][mafft] and stand-alone [BLAST][blast]

* Phylogeny tools: [RAxML][raxml]

## Version

*pG-lt is still in its developmental stage.*

## License

GPL v.2

## Authors

[Dom Bennett][db], [Will Pearse][wp], [Lawrence Hudson][lh],

[Gerard Gorman][gg] and [Andy Purvis][ap]

[db]: https://github.com/DomBennett

[wp]: https://github.com/willpearse

[lh]: https://github.com/quicklizard99

[gg]: https://github.com/ggorman

[ap]: https://github.com/AndyPurvis

[pG]: http://willpearse.github.io/phyloGenerator/

[wiki]: https://github.com/DomBennett/pG-lt/wiki

[mafft]: http://mafft.cbrc.jp/alignment/software/

[raxml]: https://github.com/stamatak/standard-RAxML

[blast]: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download