phyluce: software for UCE (and general) phylogenomics¶
Release v1.6. (Changelog)
|Author:||Brant C. Faircloth|
|Date:||31 August 2018 14:02 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 http://ultraconserved.org 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.
- Quality Control
- UCE Processing for Phylogenomics
- Tutorial I: UCE Phylogenomics
- Tutorial II: Phasing UCE data
- Tutorial III: Harvesting UCE Loci From Genomes
- Tutorial IV: Identifying UCE Loci and Designing Baits To Target Them