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r2gA homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
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usherUltrafast Sample Placement on Existing Trees
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phylonium♥ Fast and Accurate Estimation of Evolutionary Distances
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TreeSAPPA Python package for gene-centric taxonomic and functional classification using phylogenetic placement
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CAFEAnalyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
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taxoniumA tool for exploring very large trees in the browser
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FAVITESFAVITES (FrAmework for VIral Transmission and Evolution Simulation)
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BiopythonOfficial git repository for Biopython (originally converted from CVS)
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libpllPhylogenetic Likelihood Library
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archaeopteryx-jsArchaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
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CAFE5Version 5 of the CAFE phylogenetics software
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genesisA library for working with phylogenetic and population genetic data.
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PyPHLAWDPython version of PHLAWD
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phylogenetics-classA course in the theory and practice of phylogenetic inference from DNA sequence data
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phymlPhyML -- Phylogenetic estimation using (Maximum) Likelihood
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seqotronAlignment editor for Mac OS X
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BuddySuiteBioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
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get phylomarkersA pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches
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balticbaltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).
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RNeXMLImplementing semantically rich NeXML I/O in R
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