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
- 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
- Align our bait set to the extant genome sequences
- Match contigs to baits
- Get match counts and extract FASTA information
- Align the conserved locus data
- Trim the conserved locus alignments
- Remove the locus names from each alignment
- Get stats across the aligned loci
- Generate an incomplete matrix
- Prep raxml files, run raxml ML searches, and reconcile best tree w/ bootreps