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 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.
module spider phyluce to find out what environment modules are available for this application.
- HPC_PHYLUCE_DIR - installation directory
- HPC_PHYLUCE_CONF - default configuration file directory where phyluce.conf is located
- Configuration File
Phyluce is looking for the config file in a couple of default locations one of which is ~/.phyluce.conf. We provide a basic working configuration file at $HPC_PHYLUCE_CONF/phyluce.conf, which should be used automatically by phyluce executables. However, if you need to change the parameters you can copy it to your home directory with
$ ml phyluce $ cp $HPC_PHYLUCE_CONF/phyluce.conf ~/.phyluce.conf
See Phyluce Documentation about using your personal copy of phyluce.conf to make any changes you need.
UF Research Computing added a custom environment variable for Phyluce for researchers who need to provide custom MAFFT arguments. Export the
PHYLUCE_MAFFT_ARGS environment variable with the arguments e.g.
export PHYLUCE_MAFFT_ARGS="--reorder --adjustdirectionaccurately --anysymbol --maxiterate 1000 --retree 1 --genafpair"
If you publish research that uses phyluce you have to cite it as follows:
Faircloth BC. 2014. phyluce: phylogenetic estimation from ultraconserved elements. doi:10.6079/J9PHYL.
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.