title: Ultra-large alignments using phylogeny-aware profiles.
abstract: Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence alignments and phylogenetic trees of large datasets. However, accurate large-scale multiple sequence alignment is very difficult, especially when the dataset contains fragmentary sequences. We present UPP, a multiple sequence alignment method that uses a new machine learning technique, the ensemble of hidden Markov models, which we propose here. UPP produces highly accurate alignments for both nucleotide and amino acid sequences, even on ultra-large datasets or datasets containing fragmentary sequences. UPP is available at https://github.com/smirarab/sepp .
authors.affiliation: Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, 61801, Illinois, USA. namphuon@illinois.edu.
authors.forename: Nam-Phuong D
authors.initials: NP
authors.lastname: Nguyen
authors.affiliation: Department of Computer Science, University of Texas at Austin, 2505 Speedway, Austin, 78712, Texas, USA. smirarab@cs.utexas.edu.
authors.forename: Siavash
authors.initials: S
authors.lastname: Mirarab
authors.affiliation: Department of Computer Science, University of Texas at Austin, 2505 Speedway, Austin, 78712, Texas, USA. kk8@cs.utexas.edu.
authors.forename: Keerthana
authors.initials: K
authors.lastname: Kumar
authors.affiliation: Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, 61801, Illinois, USA. warnow@illinois.edu.|Department of Bioengineering, University of Illinois at Urbana-Champaign, 1270 Digital Computer Laboratory, Urbana, 61801, Illinois, USA. warnow@illinois.edu.|Department of Computer Science, University of Illinois at Urbana-Champaign, 201 North Goodwin Avenue, Urbana, 61801, Illinois, USA. warnow@illinois.edu.
authors.forename: Tandy
authors.initials: T
authors.lastname: Warnow
mesh_terms: D000465:Algorithms; D000069550:Machine Learning; D008390:Markov Chains; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*