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Align
Caio Raposo edited this page Nov 3, 2021
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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.