Phyluce

Description

phyluce website

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

Environment Modules

Run module spider phyluce to find out what environment modules are available for this application.

Environment Variables

• HPC_PHYLUCE_DIR - installation directory
• HPC_PHYLUCE_BIN - executable directory

Additional Usage Information

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"

Citation

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.

Categories

biology, ngs, sequencing