How I can get percent identity matrix from clustalw or clustalo?

Question

[Jiun]

I have a fasta file containing multiple sequences.
I can't get percentage identity matrix, despite of the option I added.

clustalo --infile={my_fasta} -t DNA --percent-id -o {out_file}

clustalw -infile={my_fasta} -type=DNA -pim -outfile={out_file}

How can I get percentage identity matrix from this software in my server?

[Jiun]

I also tried option: -pim=TRUE or -pim=True

Answer 1

[Mensur Dlakic]

The option --percent-id will tell clustalo to calculate % identity instead of distance. Normally, it calculates the distance as [1 - % identity]. You still need to specify where the matrix will be saved (the -o switch specifies where to save the alignment), and also have to force full alignment.

clustalo --infile={my_fasta} -t DNA --percent-id --full --distmat-out={matrix_file} -o {out_file}

[Jiun]

Finally I can get the matrix of percent identity. Thank you so much!! :)