User:Josiasseb/sandbox

This section is to be added to the multiple sequence alignment article.

Phylogeny-aware methods

Most multiple sequence alignment methods try to minimize the number of

First of such methods started to be developed in 2005 by Löytynoja and Goldman.^[1] The same authors released a software called PRANK in 2008.^[2] PRANK improves alignments when insertions are present. Nevertheless, it runs slowly compared to progressive and/or iterative methods developed for several years.

In 2012, two new phylogeny-aware tools appeared. One is PAGAN developed by the same team than PRANK.^[3] The other is ProGraphMSA developed by Szalkowski.^[4] Both were developed independently but share common features, notably the use of graph algorithms to improve the recognition of non-homologous regions, and an improvement in code making these software faster than PRANK.

References