phylogeny

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

DeepTime Mammalia：交互式哺乳纲演化树，3D 螺旋序幕 + D3.js 动态时间树，跨越 2 亿年 | Interactive mammalian phylogeny with 3D spiral intro & D3.js dynamic timetree spanning 200 Myr

A minimalist tree plotting library using toyplot graphs

Gotree: a set of command line tools and an API to manipulate phylogenetic trees.

A tool for exploring large trees in the browser

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

📚 a complete reference book for treeio, tidytree and ggtree packages

Goalign : a set of command line tools and an API to manipulate multiple sequence alignments.

Interactive assembly and analysis of RAD-seq data sets

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

A fast and scalable phylogenetic tree viewer for microbiome data analysis

Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

Tools for accessing the Botanical Information and Ecology Network (BIEN) database

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

A fast terminal-based viewer and command-line toolkit for molecular sequences (DNA, AA). View, translate, convert (to FASTA), and combine sequences aligned or not — all from the terminal.

Interface to Open Tree of Life API

all methods related to Enterobase

Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)

Framework for Metastatic And Clonal History INtegrative Analysis