Adding unaligned sequences into an existing alignment using MAFFT and LAST

By Kazutaka Katoh, Martin C. Frith. 2012

243 citations recorded by the source corpus.

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: katoh@ifrec.osaka-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online

Subfields: Genetics, Microbiology, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Microbiology

In Molecular Biology

Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “Details of the ––add and ––addfragments options are described in Katoh and Frith (2012).”
Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees (2016, background): “That is, a relatively accurate core alignment is ﬁrst built with an iterative reﬁnement option, G-INS-i, and then the remaining sequences are added into the core alignment as discussed in Katoh and Frith (2012).”