phyluce: software for UCE (and general) phylogenomics

Release v1.6. (Changelog)

Author:Brant C. Faircloth
Date:08 October 2019 15:48 UTC (+0000)
Copyright:This documentation is available under a Creative Commons (CC-BY) license.

phyluce (phy-loo-chee) is a software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes (see References and for additional information).

The package now includes a number of tools spanning:

  • the assembly of raw read data to contigs
  • the separation of UCE loci from assembled contigs
  • parallel alignment generation, alignment trimming, and alignment data summary methods in preparation for analysis
  • alignment and SNP calling using UCE or other types of raw-read data.

As it stands, the phyluce package is useful for analyzing both data collected from UCE loci and also data collection from other types of loci for phylogenomic studies at the species, population, and individual levels.


phyluce is open-source (see License) and we welcome contributions from anyone who is interested. Please make a pull request on github. The issue tracker for phyluce is also available on github.


If you have an issue, please ensure that you are experiencing this issue on a supported OS (see Installation) using the conda installation of phyluce. If possible, please submit a test case demonstrating the issue and indicate which platform, git checkout, and phyluce version you are using.