1. 介绍

MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.

https://mafft.cbrc.jp/

https://mafft.cbrc.jp/alignment/software/source.html

2. 使用

  1. mafft --help
  2. ## ------------------------------------------------------------------------------
  3. ##   MAFFT v7.525 (2024/Mar/13)
  4. ##   https://mafft.cbrc.jp/alignment/software/
  5. ##   MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
  6. ## ------------------------------------------------------------------------------
  7. ## High speed:
  8. ##   % mafft in > out
  9. ##   % mafft --retree 1 in > out (fast)
  10. ## 
  11. ## High accuracy (for <~200 sequences x <~2,000 aa/nt):
  12. ##   % mafft --maxiterate 1000 --localpair  in > out (% linsi in > out is also ok)
  13. ##   % mafft --maxiterate 1000 --genafpair  in > out (% einsi in > out)
  14. ##   % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)
  15. ## 
  16. ## If unsure which option to use:
  17. ##   % mafft --auto in > out
  18. ## 
  19. ## --op # :         Gap opening penalty, default: 1.53
  20. ## --ep # :         Offset (works like gap extension penalty), default: 0.0
  21. ## --maxiterate # : Maximum number of iterative refinement, default: 0
  22. ## --clustalout :   Output: clustal format, default: fasta
  23. ## --reorder :      Outorder: aligned, default: input order
  24. ## --quiet :        Do not report progress
  25. ## --thread # :     Number of threads (if unsure, --thread -1)
  26. ## --dash :         Add structural information (Rozewicki et al, submitted)

参考