Ultra-large alignments using phylogeny-aware profiles
TL
TL;DR
UPP is presented, a multiple sequence alignment method that uses a new machine learning technique, the ensemble of hidden Markov models, which produces highly accurate alignments for both nucleotide and amino acid sequences, even on ultra-large datasets or datasets containing fragmentary sequences.
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.
References53 items
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Nucleic Acids Research
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PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences
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Plos One
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Inferring phylogenies of evolving sequences without multiple sequence alignment
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