title: Adding unaligned sequences into an existing alignment using MAFFT and LAST.
abstract: 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.
  
  
  BACKGROUND
  http://mafft.cbrc.jp/alignment/software/
  
  
  BACKGROUND
  katoh@ifrec.osaka-u.ac.jp
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita 565-0871, Japan. katoh@ifrec.osaka-u.ac.jp
authors.forename: Kazutaka
authors.initials: K
authors.lastname: Katoh
authors.forename: Martin C
authors.initials: MC
authors.lastname: Frith
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D012984:Software