phyloGenerator: an automated phylogeny generation tool for ecologists

Pearse, William D.; Purvis, Andy. 2013 phyloGenerator: an automated phylogeny generation tool for ecologists. Methods in Ecology and Evolution, 4 (7). 692-698. https://doi.org/10.1111/2041-210X.12055

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Abstract/Summary

Ecologists increasingly wish to use phylogenies, but are hampered by the technical challenge of phylogeny estimation. We present phyloGenerator, an open-source, stand-alone Python program, that makes use of pre-existing sequence data and taxonomic information to largely automate the estimation of phylogenies. phyloGenerator allows nonspecialists to quickly and easily produce robust, repeatable, and defensible phylogenies without requiring an extensive knowledge of phylogenetics. Experienced phylogeneticists may also find it useful as a tool to conduct exploratory analyses. phyloGenerator performs a number of ‘sanity checks’ on users' output, but users should still check their outputs carefully; we give some advice on how to do so. By linking a number of tools in a common framework, phyloGenerator is a step towards an open, reproducible phylogenetic workflow. Bundled downloads for Windows and Mac OSX, along with the source code and an install script for Linux, can be found at http://willpearse.github.io/phyloGenerator (note the capital ‘G’) - see Related URLs

Item Type:	Publication - Article
Digital Object Identifier (DOI):	https://doi.org/10.1111/2041-210X.12055
UKCEH and CEH Sections/Science Areas:	Pywell
ISSN:	2041-210X
Additional Information. Not used in RCUK Gateway to Research.:	Full text freely available via the Official URL
Additional Keywords:	community phylogenetics, comparative analysis, phylogenetics, phylogeny construction, sequence alignment
NORA Subject Terms:	Data and Information
Related URLs:	Other
Date made live:	24 Mar 2014 09:48 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/506434

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