A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.

phylogenetics tools for linux (and other mostly posix compliant) computers

Comparative Genomics Toolkit 3

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)

Microbial Genome Circular plotting tool for comparative genomics using Circos

DFOIL: Introgression Testing for Five Taxa

A tool for plotting CAFE5 gene family expansion/contraction result

Python version of PHLAWD

Workflow for identifying and classifying homologous gene/protein sequences

Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.

Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method

A solutions manual for all excercises in the Ziheng Yang's two seminall books on statistical molecular evolution: Computational Molecular Evolution (Yang 2006) and Molecular Evolution: A Statistical Approach (Yang 2014).

phylogenetic analyses informed by deep mutational scanning data

Computational Biology & Bioinformatics Resources

Program for estimating dN/dS in overlapping genes (OLGs)

An R package to identify and classify duplicated genes from whole-genome protein sequence data

Multisample Variant Format ToolKit

A curated list of awesome Molecular Modeling And Drug Discovery 🔥

Program for simulating non-reversible DNA sequence evolution on a fixed bifurcating tree using trinucleotide context