phyluce: software for UCE (and general) phylogenomics

Release v1.7.3

Author:

Brant C. Faircloth

Date:

06 November 2024 17:41 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.

Contributions

phyluce is open-source (see License) and we welcome contributions from anyone who is interested. Please make a pull request on github.

Issues

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.

Guide

Contents:

• Purpose
  • Longer-term goals (v2.0.0+ and beyond)
  • Who wrote this?
  • How do I report bugs?
• Installation
  • Install Process
    • Using Conda
    • Using Docker
    • Using Singularity
  • phyluce configuration
  • Other useful tools
• Phyluce Tutorials
  • Tutorial I: UCE Phylogenomics
    • Download the data
    • Count the read data
    • Clean the read data
    • Assemble the data
    • Finding UCE loci
    • Extracting UCE loci
    • Aligning UCE loci
    • Alignment cleaning
    • Final data matrices
    • Preparing data for downstream analysis
    • Next Steps
  • Tutorial II: Phasing UCE data
    • Exploding aligned and trimmed UCE sequences
    • Creating a re-alignment configuration file
    • Mapping reads against contigs
    • Phasing mapped reads
  • Tutorial III: Harvesting UCE Loci From Genomes
    • Starting directory structure
    • Download the data
    • Finding UCE loci
  • Tutorial IV: Identifying UCE Loci and Designing Baits To Target Them
    • Starting directory structure
    • Data download and preparation
    • Read alignment to the base genome
    • Conserved locus identification
    • Conserved locus validation
    • Final bait set design
    • The master bait list
    • In-silico test of the bait design
• Phyluce in Daily Use
  • Quality Control
    • Read Counts
    • Adapter- and quality-trimming
  • Assembly
    • Setup
    • Running the assembly
  • UCE Processing for Phylogenomics
    • Identifying UCE loci
    • Creating a data matrix configuration file
    • Extracting FASTA data using the data matrix configuration file
    • Aligning and trimming FASTA data
    • Operations on alignments
    • Preparing concatenated alignment data for analysis
  • Workflows
    • What’s Different
    • Workflow Location
    • Workflow Configuration
    • Different Workflows
  • List of Phyluce Programs
    • Assembly
    • Alignment
    • Genetrees
    • NCBI
    • Probes
    • Utilities
    • Workflow

Project info

• Citing
• License
• Attributions
• Funding
• Acknowledgements