phyluce: software for UCE (and general) phylogenomics

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

The package now includes a number of tools spanning:

• the assembly of raw read data to contigs
• the identification of UCE 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.

Please see the Documentation for additional information on using phyluce

Installing

We strongly suggest installaing phyluce using anaconda/miniconda and the conda package manager for python. We build and test phyluce dependencies and function on the following platforms.

• Apple OSX 10.9.x
• CentOS 6.x
• Ubuntu 14.04 LTS

Quick version

1. Install JAVA for your platform
2. Install anaconda for your platform (Instructions)

3. Check that anaconda/miniconda are installed and in your $PATH:

   python -V
   Python 2.7.6 :: Anaconda 1.8.0 (x86_64)

4. Add the faircloth-lab binstar repository to your .condarc:

   conda config --add channels http://conda.binstar.org/faircloth-lab

5. Install phyluce:

   conda install phyluce

For more in-depth installation instructions, see the Installation documents.

License

3-clause BSD. See License.txt for more information.

Contributions

phyluce is open-source (see License), and we welcome contributions from anyone who is interested in contributing. To contribute code, please make a pull request on github. The issue tracker for phyluce is also available on github.

Issues

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.

Citing

If you use the phyluce code in any form, please cite the following manuscript (which is "in review"):

If you are processing UCE data that you have collected by targeted enrichment using our probes/protocols, please cite the following manuscripts, which describes the first use of the general approach:

BCF2012

BC Faircloth, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Systematic Biology 61: 717–726. doi:`10.1093/sysbio/SYS004 <http://doi.org/10.1093/sysbio/SYS004>`_.

BCF2015

Faircloth BC. 2015. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics. doi:`10.1093/bioinformatics/btv646 <10.1093/bioinformatics/btv646>`_.