MCMCtree tutorials

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

Identification of gene paralogs in genomes, and calculation of dS and dN/dS values for paralogous gene pairs

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

PAML pipeline

Clustering methods implementations in C++: Lloyd, K-Means, K-Means++, PAM

It is a powerful tool for aligning nucleotide sequences based on protein alignments, translating nucleotide sequences to protein, and generating phylogenetic trees using Biopython.

Simulates the evolution of intein invaded extein sequences based on simulated phylogenies and using a Monte-Carlo like process.

Snakemake pipeline for pairwise dN/dS estimation between two species

A python script that takes alignment file and builds a phylogeny tree.

Pipeline for running the Acomys cahirinus positive selection analysis using HyPhy aBSREL, HyPhy MEME and PAML codeml