MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc .

MAFFT version 7 Multiple alignment program for amino acid or nucleotide sequences To avoid overload, try a light-weight option , for virus genomes (2024/Aug).

MAFFT offers various multiple alignment strategies. They are classified into three types, ( a ) the progressive method, ( b ) the iterative refinement method with the WSP score, and ( c ) the iterative refinment method using both the WSP and consistency scores.

Mafft and its manpage are offered under the following conditions: Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

powershell.exe -ExecutionPolicy AllSigned C:\somewhere\mafft-win\mafft-signed.ps1 --localpair --out output.txt input.txt There are more efficient ways to directly call binary executables (.exe), instead of a script, in Windows environment.

% mafft --pileup in > out aligns the sequences just in the input order, and % mafft --randomchain in > out randomizes the order. Their accuracy is controversial. See Boyce et al. (2014) and Yamada et al. (2016) for details. Following options (Katoh & Toh 2007) are still available: % mafft --parttree --retree 1 in > out % mafft --parttree ...

Accurate options (mafft-linsi, mafft-ginsi and mafft-einsi), instead of mafft, can be used for a few hundreds of sequences. aligned_sequences must form a monophyletic cluster, as they are converted into a single profile.

How to install MAFFT without being root; Building an MSA from partial MSA(s) and unaligned sequences --seed--add, --addfragments, --addprofile--merge; Regional re-alignment. MAFFT alignments are TOO LONG! The difference between a default parameter of old versions (--ep 0.123) and that of the current version (--ep 0.0)

MAFFT version 7 Multiple alignment program for amino acid or nucleotide sequences. Three versions for Windows. Ubuntu version; Includes text-based interactive mode for basic functions and command-line mode for full functionality. Faster than the other two packages for Windows.

The mafft program can be placed in any folder in your mac. Administrator privileges are not necessary, if you place this package somewhere in your home folder. Aliases ( mafft-linsi , etc) are not available.