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

TitlePASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.
Publication TypeJournal Article
Year of Publication2015
AuthorsMirarab S, Nguyen N, Guo S, San Wang L-, Kim J, Warnow T
JournalJ Comput Biol
Volume22
Issue5
Pagination377-86
Date Published2015 May
ISSN1557-8666
KeywordsAlgorithms, Amino Acid Sequence, Bacteria, Base Sequence, Computer Simulation, Datasets as Topic, Evolution, Molecular, Metagenomics, Molecular Sequence Data, Phylogeny, Plants, Sequence Alignment, Software
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.

DOI10.1089/cmb.2014.0156
Alternate JournalJ. Comput. Biol.
PubMed ID25549288
PubMed Central IDPMC4424971
Grant ListR01-GM099962 / GM / NIGMS NIH HHS / United States
R01 GM099962 / GM / NIGMS NIH HHS / United States
T32-HG000046 / HG / NHGRI NIH HHS / United States
U24-AG041689 / AG / NIA NIH HHS / United States
/ / Howard Hughes Medical Institute / United States