Phylogeny-aware Methods
Most multiple sequence alignment methods try to minimize the number of insertions/deletions (gaps) and, as a consequence, produce compact alignments. This causes several problems if the sequences to be aligned contain non-homologous regions, if gaps are informative in a phylogeny analysis. These problems are common in newly produced sequences that are poorly annotated and may contain frame-shifts, wrong domains or non-homologous spliced exons.
The first such method was developed in 2005 by Löytynoja and Goldman. The same authors released a software package called PRANK in 2008. PRANK improves alignments when insertions are present. Nevertheless, it runs slowly compared to progressive and/or iterative methods which have been developed for several years.
In 2012, two new phylogeny-aware tools appeared. One is called PAGAN that was developed by the same team as PRANK. The other is ProGraphMSA developed by Szalkowski. Both software packages 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.
Read more about this topic: Multiple Sequence Alignment
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