使用 MAFFT 和 LAST 将未对齐的序列添加到现有比对中。
Adding unaligned sequences into an existing alignment using MAFFT and LAST.
机构信息
Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita 565-0871, Japan.
出版信息
Bioinformatics. 2012 Dec 1;28(23):3144-6. doi: 10.1093/bioinformatics/bts578. Epub 2012 Sep 27.
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
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
未标记
两种将未对齐序列添加到现有多重序列比对中的方法已在 MAFFT 包中实现，即“--add”和“--addfragments”选项。前者是基本选项，仅适用于全长序列，而后者即使未对齐序列较短且零碎也适用。这些方法内部推断现有比对中序列之间的系统发育关系以及未对齐序列的系统发育位置。基于两个独立模拟的基准测试一致表明，“--addfragments”选项在准确性方面优于最近的方法 PaPaRa 和 PAGAN，适用于困难问题，并且这三种方法适当地处理简单问题。
可用性
http://mafft.cbrc.jp/alignment/software/
联系人
补充信息
补充材料可在Bioinformatics 在线获得。
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