forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research
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Updated
May 29, 2024 - Java
forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research
Thesis projects
Comparative Genomics Toolkit 3
Official git repository for Biopython (originally converted from CVS)
R package for phylogenetic tree search under custom optimality criteria
Create, modify and analyse phylogenetic trees in R
Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconcillation levels
Light phylogeny API for Rust
Molecular Evolution Library for Python
Tool for fully-automated inference of species trees from raw genome assemblies
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.
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
Project based on GrapeTree, a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metadata.
Evaluating the Use of Bulk and Single-Cell Sequences in Phylogenetic Analyses of Multi-tumour Evolution
Phylogenetic tree maker for alignment and phylogeny inference. Performs global and local sequence alignments using the Needleman-Wunsch and Smith-Waterman algorithms, followed by tree construction via the Neighbor-Joining method.
Bayesian Evolutionary Analysis Sampling Trees
R package to calculate the similarity of two trees based on the number of shared four-taxon subtrees (or splits)
Bayesian Evolutionary Analysis by Sampling Trees
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