phyloGenerator: an automated phylogeny generation tool for ecologists
Article first published online: 16 MAY 2013
© 2013 The Authors. Methods in Ecology and Evolution © 2013 British Ecological Society
Methods in Ecology and Evolution
Volume 4, Issue 7, pages 692–698, July 2013
How to Cite
Pearse, W. D., Purvis, A. (2013), phyloGenerator: an automated phylogeny generation tool for ecologists. Methods in Ecology and Evolution, 4: 692–698. doi: 10.1111/2041-210X.12055
- Issue published online: 2 JUL 2013
- Article first published online: 16 MAY 2013
- Accepted manuscript online: 26 MAR 2013 06:40AM EST
- Manuscript Accepted: 27 FEB 2013
- Manuscript Received: 5 FEB 2013
- community phylogenetics;
- comparative analysis;
- phylogeny construction;
- sequence alignment
- 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’).