Helper scripts for processing and visualization of phylogenetics datasets, mostly written in Python. For more information about each of the scripts, visit the appropriate subdirectory.
Python and shell scripts for phasing alleles from HybSeq data, as done in Kates et al. AJB 2018.
Script for plotting pie charts from bipartition analysis on a species phylogeny.
Scripts for working with target capture data recovered or assembled using HybPiper, including fasta_merge.py from version 1.3.1.
Display minority bipartitions on a species tree.
Adjust phased allelic sequences to have phased alleles only in the largest phase block, with ambiguity codes elsewhere. Used in Kates et al. AJB 2018
Identify extreme branch lengths in a set of gene trees. Generates images of offending trees so that manual curation of every gene tree is not necessary.