Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Phylogenetic analysis in R

LinguaPhylo: A language for describing, visualising and simulating probabilistic phylogenetic models

Script for removing or counting invariant sites for the RAxML ascertainment bias corrections

A Modular and Web-Based Tool for Phylogenetic Analysis

Tool for estimating the Felsenstein bootstrap support of phylogenetic trees

R htmlwidget for Jellyfish

Jellyfish plots for integrative visualization of spatio-temporal tumor evolution and clonal dynamics

a tool for automatic construction of molecular data matrix for phylogenetic inference based on GenBank records

A comparative annotation toolkit (CAT) pipeline for 304 fly genomes.

Phylogenetic Inference and Data Visualization for Sequence-Based Typing Methods

An R package to prepare data for phylogenetic analysis

Genomic Epidemiology of SARS-CoV-2 in Pakistan

GRAPPA: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms

A Framework for Large Scale Phylogenetic Analysis

FUSE-PhyloTree enables to identify sequence conservation modules and associate them with functional annotations through phylogenomic analysis.

Morphy releases are archived here. This project serves as the root folder for all of the source projects in Morphy.

A phylogenetically-aware framework for detecting evolutionary associations between binary traits

An in vivo PRA reveals intronic motifs that combinatorially regulate splicing in a tissue-biased manner.

COEDL Summer School 2019 - Language Phylogenies Tutorial