MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

Molecular Biology and Evolution
Vincent RanwezFrédéric Delsuc

Abstract

Multiple sequence alignment is a prerequisite for many evolutionary analyses. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that explicitly accounts for the underlying codon structure of protein-coding nucleotide sequences. Its unique characteristic allows building reliable codon alignments even in the presence of frameshifts. This facilitates downstream analyses such as selection pressure estimation based on the ratio of nonsynonymous to synonymous substitutions. Here, we present MACSE v2, a major update with an improved version of the initial algorithm enriched with a complete toolkit to handle multiple alignments of protein-coding sequences. A graphical interface now provides user-friendly access to the different subprograms.

References

Aug 10, 2002·Bioinformatics·Michael HöhlEnno Ohlebusch
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jul 25, 2007·Bioinformatics·Travis J Wheeler, John D Kececioglu
Sep 12, 2008·Molecular Ecology Notes·Sujeevan Ratnasingham, Paul D N Hebert
Oct 26, 2012·Genome Biology and Evolution·Raquel AssisDoris Bachtrog
Apr 12, 2014·Molecular Biology and Evolution·Emmanuel J P DouzeryVincent Ranwez
Jul 29, 2015·Molecular Ecology Resources·Jason G BraggCraig Moritz

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Citations

Jan 31, 2019·Molecular Biology and Evolution·Celine ScornavaccaVincent Ranwez
May 7, 2019·Molecular Biology and Evolution·Craig F BarrettAaron H Kennedy
Aug 17, 2019·Evolution; International Journal of Organic Evolution·Raquel Assis
Mar 15, 2020·Molecular Biology and Evolution·Rodrigo PracanaPeter W H Holland
Apr 3, 2020·Journal of Virology·Veronika KrchlíkováDaniel Elleder
Dec 18, 2019·BMC Bioinformatics·Esaie KuitcheAïda Ouangraoua
May 26, 2020·Nucleic Acids Research·Luís Q AlvesL Filipe C Castro
Jul 28, 2019·ELife·Aaron A VoganHanna Johannesson
Jul 28, 2019·Ecology and Evolution·Shamshidin AbduriyimHuabin Zhao
Oct 21, 2020·BMC Evolutionary Biology·Yichen DaiPeter W H Holland
Oct 13, 2020·Molecular Biology and Evolution·Michael DeGiorgio, Raquel Assis
Oct 22, 2020·Molecular Ecology Resources·Lily C HughesRicardo Betancur-R
Feb 1, 2020·International Journal of Biological Macromolecules·Jiajia WangMaofa Yang
Jan 9, 2021·FEMS Yeast Research·Sheila Tiemi NagamatsuMarcelo Falsarella Carazzolle
Nov 11, 2020·Molecular Plant·Aline MuyleAlexandros Bousios
Oct 30, 2020·International Journal of Molecular Sciences·Saipeng ChengZhenhai Chen
Nov 20, 2020·Nature·Fabrizia RoncoWalter Salzburger
Jan 22, 2021·Current Biology : CB·Thibault LeroyBenoit Nabholz
Mar 10, 2021·Communications Biology·Ousmane H CisséJoseph A Kovacs
Mar 15, 2021·G3 : Genes - Genomes - Genetics·Andreina I Castillo, Rodrigo P P Almeida
May 16, 2021·BMC Ecology and Evolution·Adrielle A VasconcelosRenata M Baroni
Apr 7, 2021·Molecular Biology and Evolution·Benjamin LinardUNKNOWN QFO Consortium
Jun 26, 2021·Current Biology : CB·Luís Q AlvesL Filipe C Castro
Feb 25, 2021·Molecular Biology and Evolution·M V WestburyMichael Hofreiter

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Methods Mentioned

BETA
RNAseq

Software Mentioned

MACSE
HMMcleaner
OMM
SeaView
MIDORI
MUSCLE

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