Work

Adding unaligned sequences into an existing alignment using MAFFT and LAST

Year: 2012

Type: article

Abstract: UNLABELLED: Two methods to add unaligned sequences into an existing multiple sequence alignment have been implemented as the '--add' and '--addfragments' options in the MAFFT package. The former option is a basic one and applicable only to full-length sequences, whereas the latter option is applicable even when the unaligned sequences are short and fragmentary. These methods internally infer the phylogenetic relationship among the sequences in the existing alignment and the phylogenetic positions of unaligned sequences. Benchmarks based on two independent simulations consistently suggest that the "--addfragments" option outperforms recent methods, PaPaRa and PAGAN, in accuracy for difficult problems and that these three methods appropriately handle easy problems. AVAILABILITY: http://mafft.cbrc.jp/alignment/software/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/bts578

Authors: Kazutaka Katoh, Martin C. Frith

Institutions: Immunology Frontier Research Center, The University of Osaka, The University of Osaka, National Institute of Advanced Industrial Science and Technology

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $3,989

Funder: Japan Society for the Promotion of Science