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

Microbial Genome Circular plotting tool for comparative genomics using Circos

A tool for plotting CAFE5 gene family expansion/contraction result

DFOIL: Introgression Testing for Five Taxa

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

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).

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.

Computational Biology & Bioinformatics Resources

phylogenetic analyses informed by deep mutational scanning data

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

A curated list of awesome Molecular Modeling And Drug Discovery 🔥

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.