MAFFT version 7 - Multiple alignment program for amino acid or nucleotide sequences
Location and version:
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$ which mafft
/local/cluster/mafft/bin/mafft
$ mafft --version
v7.487 (2021/Jul/25)
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help message:
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$ mafft --help
------------------------------------------------------------------------------
MAFFT v7.487 (2021/Jul/25)
https://mafft.cbrc.jp/alignment/software/
MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
------------------------------------------------------------------------------
High speed:
% mafft in > out
% mafft --retree 1 in > out (fast)
High accuracy (for <~200 sequences x <~2,000 aa/nt):
% mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok)
% mafft --maxiterate 1000 --genafpair in > out (% einsi in > out)
% mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)
If unsure which option to use:
% mafft --auto in > out
--op # : Gap opening penalty, default: 1.53
--ep # : Offset (works like gap extension penalty), default: 0.0
--maxiterate # : Maximum number of iterative refinement, default: 0
--clustalout : Output: clustal format, default: fasta
--reorder : Outorder: aligned, default: input order
--quiet : Do not report progress
--thread # : Number of threads (if unsure, --thread -1)
--dash : Add structural information (Rozewicki et al, submitted)
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This program, especially the L-INS-i algorithm for most proteins, is exceptional
at producing high quality alignments.
I recommend using the --thread and --reorder options, along with linsi as
the alignment command.
software ref: https://mafft.cbrc.jp/alignment/software/
research ref: https://academic.oup.com/mbe/article/30/4/772/1073398