phylogenetic-analysis

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

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

Phylogenetic Inference and Data Visualization for Sequence-Based Typing Methods

Tool for estimating the Felsenstein bootstrap support of phylogenetic trees

R htmlwidget for Jellyfish

bifrost is an R package for detecting shifts in multivariate evolutionary dynamics on phylogenies

A comparative annotation toolkit (CAT) pipeline for 301 Drosophila genomes.

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

An R package to prepare data for phylogenetic analysis

This tool provides a modular WDL-Docker-Cromwell environment for rMAP, a bioinformatics pipeline for analyzing microbial genomic data, genome assembly & profiling of the resistome, mobilome & virulome, as well as pangenome & MLST typing, BLASTn & phylogenetic analysis. It includes all required tools, enabling reproducible & scalable analysis

Genomic Epidemiology of SARS-CoV-2 in Pakistan

GRAPPA: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms

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

Analyzing the genomic and metagenomic features of SGB748 MAGs from oral samples to uncover their role in health and peri-implant diseases through patient metadata integration.

A Framework for Large Scale Phylogenetic Analysis