Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. Over the last ...

This paper introduces a simple and effective approach to improve the accuracy of multiple sequence alignment. We use a natural measure to estimate the similarity of the input sequences, and based on ...

FMAlign2 is a novel multiple sequence alignment algorithm based on FMAlign. It is designed to efficiently align ultra-long nucleotide sequences fast and accurately.

A simple Python script to generate a multiple sequence alignment (FASTA, NEXUS, PHYLIP, etc.) from a VCF/BCF file. For those occasions when a program requires an alignment in plain text, or you simply ...

Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a ...