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, part of Kates et al. AJB in review.

Script for plotting pie charts from bipartition analysis on a species phylogeny.

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.

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.