26 Open source projects that are alternatives of or similar to CAFE

A tool for exploring very large trees in the browser

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

Official git repository for Biopython (originally converted from CVS)

Phylogenetic Likelihood Library

Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.

Phylogenetic trees in Julia

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

Version 5 of the CAFE phylogenetics software

A library for working with phylogenetic and population genetic data.

Python version of PHLAWD

A course in the theory and practice of phylogenetic inference from DNA sequence data

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

Alignment editor for Mac OS X

Ancestor character reconstruction and visualisation for rooted phylogenetic trees

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

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).

Implementing semantically rich NeXML I/O in R

Biological Sequence Substitution Models for Julia

booster.c3bi.pasteur.fr

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

Ultrafast Sample Placement on Existing Trees

Sequential Tree Sampler for online phylogenetics

♥ Fast and Accurate Estimation of Evolutionary Distances

A Python package for gene-centric taxonomic and functional classification using phylogenetic placement