https://github.com/lukasturcani/stk

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

cheminformatics chemistry computational-chemistry computational-science materials-design materials-discoveries materials-science materials-screening molecular-evolution molecular-modeling molecular-structures reactions

Last synced: 04 Apr 2025

https://github.com/cogent3/cogent3

Comparative Genomics Toolkit 3

bioinformatics biological-sequence-analysis biology biopython data-science evolution genomics markov-chain maximum-likelihood molecular-evolution non-stationary parallel phylogenetic-trees phylogenetics pycogent python sequence-alignment signal-processing statistics

Last synced: 20 Apr 2026

https://github.com/chasewnelson/snpgenie

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

diversity-measurement dnds dnds-estimation evolution evolutionary-parameters fasta-sequences molecular-evolution natural-selection nei-gojobori next-generation-sequencing nucleotide nucleotide-diversity perl population-genetics sequence-analysis snp-report substitution-rate vcf vcf-files

Last synced: 23 Mar 2025

https://github.com/lkremer/cafe_fig

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

cafe ete3 evolution gene-families molecular-evolution phylogenetic-trees

Last synced: 09 May 2025

https://github.com/almeidasilvaf/doubletrouble

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

bioinformatics comparative-genomics gene-duplication molecular-evolution rstats whole-genome-duplication

Last synced: 23 Feb 2026

https://github.com/moshi4/cafeplotter

A tool for plotting CAFE5 gene family expansion/contraction result

bioinformatics evolution matplotlib molecular-evolution phylogenetic-trees phylogenetics phylogenomics python

Last synced: 21 Apr 2025

https://github.com/lkremer/msa_trimmer

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

aligned-regions alignment-trimming cds-alignment codeml codon-alignment molecular-evolution msa-trimmer multiple-sequence-alignment paml phylogenetics sequence-alignment trimmer trimming

Last synced: 06 Jul 2025

https://github.com/JRaviLab/compbio-gists

Computational Biology & Bioinformatics Resources

bioinformatics comparative-genomics computational-biology data-science gists molecular-evolution phylogeny r shell transcriptomics

Last synced: 07 Oct 2025

https://github.com/chasewnelson/OLGenie

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

dnds dnds-estimation molecular-evolution natural-selection nei-gojobori neutral-evolution overlapping overlapping-genes perl positive-selection purifying-selection selection

Last synced: 23 Mar 2025

https://github.com/smithsonian/fabaceae_phylogenomics_workflow

Target-enrichment data processing in legumes

legumes molecular-evolution phylogenetics target-enrichment

Last synced: 07 Feb 2026

https://github.com/wesleybeckner/gains

project that enables molecular design and computational screening of small molecules

machine-learning molecular-evolution rdkit

Last synced: 27 Apr 2025

https://github.com/jamesjcai/mbetoolbox

MBEToolbox: Matlab toolbox for molecular evolution

matlab maximum-likelihood molecular-evolution phylip

Last synced: 02 Jul 2025

https://github.com/chenyangkang/fasta2codeml

A codeml (PAML package) wrapper to make life easier. Dummy input unaligned multi-species fasta file (a single gene), and output codeml result.

codeml ecology molecular-evolution natural-selection paml selection

Last synced: 07 Apr 2026

https://github.com/gawbul/gawbul.github.io

Homepage of Dr Stephen P. Moss, Computational Scientist

bioinformatics computational-biology computational-genomics computational-science computing gawbul genomics homepage medicine molecular-evolution research science website

Last synced: 02 Jan 2026

https://github.com/jmenglund/predsim

Simulate predictive datasets from MrBayes' output

bayesian dendropy dna-sequences molecular-evolution mrbayes phylogenetics posterior-predictive seq-gen simulation

Last synced: 18 Mar 2025

https://github.com/jananiravi/2020-molevol-phylogeny

Supporting material for the "Molecular Evolution and Phylogeny" lecture | Feb 27, 2020

computational-biology michigan-state-university molecular-evolution phylogeny

Last synced: 05 Jan 2026

https://github.com/jananiravi/papers

comparative-genomics computational-biology host-pathogen molecular-evolution mycobacterium-tuberculosis phylogeny stress-response

Last synced: 04 Jan 2026