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

MCMCtree tutorials

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

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

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.

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