Phylogeny Tools

Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.

Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.

QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.

TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.

The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.

Block Mapping and Gathering using Entropy. BMGE was designed to select regions in a multiple sequence alignment that are suited for phylogenetic inference.

The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.

ClonalFrameML is a maximum likelihood implementation of the Bayesian software ClonalFrame which was previously described by Didelot and Falush (2007). The recombination model underpinning ClonalFrameML is exactly the same as for ClonalFrame, but this new implementation is a lot faster, is able to deal with much larger genomic dataset, and does not suffer from MCMC convergence issues

Coinfinder (pronounced "coin-finder") is an algorithm and software tool that detects genes which associate and dissociate with other genes more often than expected by chance in pangenomes. Coinfinder is written primarily in C++ and is a command line tool which generates text, gexf, and pdf outputs for the user. Coinfinder uses a Bonferroni-corrected Binomial exact test statistic of the expected and observed rates of gene-gene association to evaluate whether a given gene pair is coincident.

Fast calculation of the ABBA-BABA statistics across many populations/species.