Difference between revisions of "Phyluce"
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==System Variables== | ==System Variables== | ||
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_CONF - default configuration file directory where phyluce.conf is located | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 14:12, 15 February 2017
Description
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.
Required Modules
System Variables
- HPC_{{#uppercase:phyluce}}_DIR - installation directory
- HPC_{{#uppercase:phyluce}}_CONF - default configuration file directory where phyluce.conf is located
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.