1. Introduction:

MAFFT profile
The most classic and widely known multi-sequence alignment software is Clustalw. Comparison speed (Muscle>MAFFT>ClustalW> t-coffee), comparison accuracy (MAFFT>Muscle> t-coffee >ClustalW). Therefore, MAFFT software is recommended for multiple sequence alignment.

2.Detailed software installation and parameters:

The installation

conda install -c bioconda mafft

High speed:

mafft all.fasta > output mafft --retree 1 in > out (fast)

High accuracy (for <~200 sequences x <~2,000 AA /nt) Three different comparison methods:

mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok)

the most accurate method. Suitable for sequences less than 200 and less than 2000AA /nt in length

mafft --maxiterate 1000 --genafpair in > out (% einsi in > out)

The ### is suitable for sequences containing large unmatched regions, less than 200, and less than 2000AA /nt in length

mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)

Suitable for sequences with similar length alignment, less than 200 and less than 2000AA /nt
If unsure which option to use:

mafft --auto in > out

-- Maxiterate: Maximum number of iteration optimizations, default: 0 -- Clustalout: output: Clustal format, default: Fasta -- Reorder: out of order: align, default: input order -Quiet: Don't report progress -- Thread: Number of threads (if not sure, -- Thread-1)

3. Output Results:

The results are shown in the figure below. According to the longest sequence, mark the aa of the corresponding position. Where there is a gap, fill it out with —.
image.png