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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.
Clustering methods implementations in C++: Lloyd, K-Means, K-Means++, PAM
Simulates the evolution of intein invaded extein sequences based on simulated phylogenies and using a Monte-Carlo like process.
It is a powerful tool for aligning nucleotide sequences based on protein alignments, translating nucleotide sequences to protein, and generating phylogenetic trees using Biopython.