Phylogeny Python Packages

phylotrackpy

Python phylogeny tracker for in silico evolution experiments

phylotreelib

Library for analyzing and manipulating phylogenetic trees

taxoniumtools

A tool for exploring large trees in the browser

sumt

Computes consensus trees and other phylogenetic tree summaries

figtreekit

Programmatic styling of phylogenetic trees for FigTree visualization

prophyle

Accurate, resource-frugal and deterministic DNA sequence classifier.

phylo3d-trait

Interactive 3D phylogenetic tree visualizer for continuous trait evolution and supplied ancestral-state estimates; standalone WebGL2 HTML.

bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

empress

A fast and scalable phylogenetic tree viewer for microbiome data analysis

pyiwe

Python wrapper for TNT (Tree analysis using New Technology) implied weighting with clades support

treedist

Computes measures of (dis)similarity between phylogenetic trees. Provides summaries of shared and unique bipartitions.

oggmap

oggmap is a python package to extract orthologous maps (short: orthomap or in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Oggmap results (gene ages per orthologous group) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.