phyloGenerator: an automated phylogeny generation tool for ecologists
Correspondence author. E-mail: email@example.com
- 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’).