PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

Content Provider	Europe PMC
Author	Mirarab, Siavash Nguyen, Nam Guo, Sheng Wang, Li-San Kim, Junhyong Warnow, Tandy
Copyright Year	2015
Abstract	Abstract We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate—slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.
Related Links	https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4424971&blobtype=pdf
Page Count	10
ISSN	10665277
Volume Number	22
DOI	10.1089/cmb.2014.0156
PubMed Central reference number	PMC4424971
Issue Number	5
PubMed reference number	25549288
Journal	Journal of Computational Biology [J Comput Biol]
e-ISSN	15578666
Language	English
Publisher	Mary Ann Liebert, Inc.
Publisher Date	2014-12-30
Publisher Place	USA
Access Restriction	Open
Rights License	Copyright 2015, Mary Ann Liebert, Inc.
Subject Keyword	algorithms metagenomics molecular evolution multiple alignment phylogenetic trees
Content Type	Text
Resource Type	Article
Subject	Genetics Molecular Biology Computational Theory and Mathematics Modeling and Simulation Computational Mathematics