phyluce: software for UCE (and general) phylogenomics¶
|Author:||Brant C. Faircloth|
|Date:||25 August 2023 18:27 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 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
- SNP calling and contig correction using 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.
The issue tracker for phyluce is available on github. 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. When submitting issues, please include a test case demonstrating the issue and indicate which operating system and phyluce version you are using.
- Phyluce Tutorials
- 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
- Phyluce in Daily Use
- Quality Control
- UCE Processing for Phylogenomics
- List of Phyluce Programs