Align

Extraction and Alignment of UCEs

This is most of the steps described at PHYLUCE's Tutorial, all the commands were aggregated into the align command and you will need to provide the contigs directory at "assemblies/contigs", the set of UCE probes to use, which in this example is Tetrapods-UCE-2.5Kv1 (probes.fasta) described as part of Faircloth et al. 2012, and the completeness percentage of the final data matrices, we will also use the optional flags --incomplete-matrix and --internal-trimming.

$ uceasy align --incomplete-matrix --internal-trimming assemblies/contigs/ probes.fasta

All the data produced by the pipeline will be in the "alignments" directory.