鸟类基因组及演化生物学研究

超大规模比对

文章引用

Nam-phuong D. Nguyen, Siavash Mirarab, Keerthana Kumar and Tandy Warnow, 'Ultra-large alignments using Phylogeny-aware Profiles', Genome Biol. (2015).

英文摘要

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.

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