teiphy
teiphy: A Python Package for Converting TEI XML Collations to NEXUS and Other Formats - Published in JOSS (2022)
treemaker
treemaker: A Python tool for constructing a Newick formatted tree from a set of classifications. - Published in JOSS (2018)
Phylogemetric
Phylogemetric: A Python library for calculating phylogenetic network metrics - Published in JOSS (2016)
biopython
Official git repository for Biopython (originally converted from CVS)
gtdbtk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Lexedata
Lexedata: A toolbox to edit CLDF lexical datasets - Published in JOSS (2022)
ete3
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
TreeSearch
R package for phylogenetic tree search under inapplicable-corrected parsimony and custom optimality criteria
Quartet
R package to calculate the similarity of two trees based on the number of shared four-taxon subtrees (or splits)
trisicell
Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data
beautier
R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2
unicore
Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5
clipkit
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
daisiemainland
Simulate phylogenetic data on islands with a evolving mainland pool
phyloplace
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
orthofisher
a broadly applicable tool for automated gene identification and retrieval
phylo.jl
Simple phylogenetic trees in Julia to work with Diversity.jl - https://github.com/EcoJulia/Diversity.jl
https://github.com/4ment/torchtree
A probabilistic framework in PyTorch for phylogenetic models
paleobuddy
paleobuddy: an R package for simulating diversification dynamics, fossil records and phylogenies in R.
baltic
baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).
splitp
Python package that implements split- and rank-based tools for inferring phylogenies, such as flattenings and subflattenings.
https://github.com/4ment/physher
A multi-algorithmic framework for phylogenetic inference
phylobase
An R package that provides a base S4 class for comparative methods, incorporating one or more trees and trait data
https://github.com/cjabradshaw/coelacanthevolution
Analyses of coelacanth morphometrics, disparity, phylogeny, and rate of evolution
https://github.com/broadinstitute/vectreeid
Amplicon taxonomic identification pipeline for Neafsey Lab
phylosamp
The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linkage and sample size calculations for phylogenetic studies.
phylotoast
Tools for phylogenetic data analysis including visualization and cluster-computing support.
aniclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
https://github.com/biojulia/substitutionmodels.jl
Biological Sequence Substitution Models for Julia
https://github.com/4ment/marginal-experiments
19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology
https://github.com/4ment/torchtree-physher
https://github.com/4ment/torchtree-bito
https://github.com/4ment/torchtree-tensorflow
https://github.com/4ment/gradient-benchmark
automatic/analytical differentiation benchmark
phylo-workflow
Analytical 'point and click' scripts for phylogenetic analysis to ensure reproducibility of results
traitblender
Blender addon for simulating raw datasets under known evolutionary models
https://github.com/bionf/phylorbf
phageproteomictree
The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
traitlab
TraitLab: a Matlab toolbox for fitting and simulating binary tree-like data
SNaQ
Julia package for the inference of semi-directed phylogenetic networks under pseudolikelihood model
https://github.com/biocore/q2-qemistree
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
https://github.com/4ment/torchtree-experiments
https://github.com/biodataanalysisgroup/kmeranalyzer
An alignment-free method capable of processing and counting k-mers in a reasonable time, while evaluating multiple values of the k parameter concurrently.
https://github.com/cdcgov/microbetrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
https://github.com/4ment/torchtree-scipy
Package providing extra functionalities from SciPy
automated-window-sliding
Bioinformatics pipeline using a sliding window approach to create a sequence of trees from multiple sequence alignments.
https://github.com/compevol/beast2
Bayesian Evolutionary Analysis by Sampling Trees
derip2
Reconstruct ancestral state sequences of fungal repeat families by correcting for RIP-like mutations. Mask RIP or deamination events from alignments.
<code>diverse-seq</code>
<code>diverse-seq</code>: an application for alignment-free selecting and clustering biological sequences - Published in JOSS (2025)
https://github.com/4ment/cladokit
A minimal, no-frills C++17 library for phylogenetic trees
treespace-metrics
Python code to compute metrics on Rooted Phylogenetic Networks
https://github.com/huttleylab/phylim
Python project to validate a phylogenetic fitted models is within the limits of inference
mpox-seek
A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing