Adam M Szalkowski1. 1. Department of Computer Science, ETH Zürich, Universitätstrasse, Switzerland. adam.szalkowski@inf.ethz.ch
Abstract
BACKGROUND: ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide tree. RESULTS: This is achieved by incorporating a graph-based sequence representation combined with the advantages of the phylogeny-aware gap placement algorithm of Prank. Further, we account for variations in the substitution pattern by implementing context-specific profiles as in CS-Blast and by estimating amino acid frequencies from input data. CONCLUSIONS: ProGraphMSA shows good performance and competitive execution times in various benchmarks.
BACKGROUND: ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide tree. RESULTS: This is achieved by incorporating a graph-based sequence representation combined with the advantages of the phylogeny-aware gap placement algorithm of Prank. Further, we account for variations in the substitution pattern by implementing context-specific profiles as in CS-Blast and by estimating amino acid frequencies from input data. CONCLUSIONS: ProGraphMSA shows good performance and competitive execution times in various benchmarks.
Authors: Linnéa Smeds; Vera Warmuth; Paulina Bolivar; Severin Uebbing; Reto Burri; Alexander Suh; Alexander Nater; Stanislav Bureš; Laszlo Z Garamszegi; Silje Hogner; Juan Moreno; Anna Qvarnström; Milan Ružić; Stein-Are Sæther; Glenn-Peter Sætre; Janos Török; Hans Ellegren Journal: Nat Commun Date: 2015-06-04 Impact factor: 14.919
Authors: Sarit Weissmann; Pu Huang; Madeline A Wiechert; Koki Furuyama; Thomas P Brutnell; Mitsutaka Taniguchi; James C Schnable; Todd C Mockler Journal: Genome Biol Evol Date: 2021-02-03 Impact factor: 3.416