Helper scripts for processing and visualization of phylogenetics datasets
Switch branches/tags
Nothing to show
Clone or download

README.md

phyloscripts by mossmatters


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.

Alleles Workflow

Python and shell scripts for phasing alleles from HybSeq data, part of Kates et al. AJB in review.

PhypartsPieCharts

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

Minority Report

Display minority bipartitions on a species tree.

Haplonerate

Adjust phased allelic sequences to have phased alleles only in the largest phase block, with ambiguity codes elsewhere.

Branch Length Outlier

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.