Genome wide orthology inference and dNdS estimation

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

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

Simple code for PS detection, can be used on several files

Codon-based alignment for CDS sequences

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