PhyIN sequence alignment trimming
Version 1.0 November 2024
Wayne Maddison
This is a secondary release of the PhyIN method for trimming alignments for phylogenomics work. It includes the standalone phython code.
The primary release of PhyIN is in Java within the Mesquite environment (http://www.mesquiteproject.org), from which the snippet included here is derived. However, I provide this python code for use in bioinformatics pipelines.
It is currently built to handle only nucleotide data and fasta files.