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.
https://github.com/cran-task-views/phylogenetics
CRAN Task View: Phylogenetics
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/4ment/flc
Local clock model using relaxed and strict clocks
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
bioinformatics-toolbox
Docker container for bioinformatics tools and pipelines
SNaQ
Julia package for the inference of semi-directed phylogenetic networks under pseudolikelihood model
phylo-workflow
Analytical 'point and click' scripts for phylogenetic analysis to ensure reproducibility of results
https://github.com/4ment/torchtree-scipy
Package providing extra functionalities from SciPy
phageproteomictree
The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
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/4ment/cladokit
A minimal, no-frills C++17 library for phylogenetic trees
traitblender
Blender addon for simulating raw datasets under known evolutionary models
https://github.com/cdcgov/microbetrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
https://github.com/compevol/beast2
Bayesian Evolutionary Analysis by Sampling Trees
https://github.com/bionf/phylorbf
mpox-seek
A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing
DAISIEprep
Extracts phylogenetic island community data from phylogenetic trees
https://github.com/huttleylab/phylim
Python project to validate a phylogenetic fitted models is within the limits of inference
https://github.com/4ment/torchtree-experiments
derip2
Reconstruct ancestral state sequences of fungal repeat families by correcting for RIP-like mutations. Mask RIP or deamination events from alignments.
traitlab
TraitLab: a Matlab toolbox for fitting and simulating binary tree-like data
automated-window-sliding
Bioinformatics pipeline using a sliding window approach to create a sequence of trees from multiple sequence 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/biocore/q2-qemistree
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
treespace-metrics
Python code to compute metrics on Rooted Phylogenetic Networks