molecular-evolution

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

Comparative Genomics Toolkit 3

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

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)

Analyzing combinations of codon substitution histories

A tool for plotting CAFE5 gene family expansion/contraction result

Microbial Genome Circular plotting tool for comparative genomics using Circos

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

DFOIL: Introgression Testing for Five Taxa

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).

Conditionally Site-Independent Neural Evolution of Antibody Sequences (ICML '26)

Python version of PHLAWD

Workflow for identifying and classifying homologous gene/protein sequences

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

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

Ancestral sequence reconstruction with gap-state inference using IQ-TREE

Computational Biology & Bioinformatics Resources

phylogenetic analyses informed by deep mutational scanning data

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