I have a fasta file with amino acid sequences. Now I want to align every sequence with every other (so it's pairwise). The outcome should be a distance (or similarity, doesn't matter) matrix.
I would like to do local alignment. EDIT: The sequences do NOT have the same length and might just have similar regions partially.
What tool would you suggest?
Ideally I can later do the same with nucleotide sequences.
4 answers
Are you really sure you need a pairwise alignment and cannot do a global alignment? It is 1000 times faster and easier.
Use R! https://cran.r-project.org/web/packages/phangorn/phangorn.pdf Page 20
library(ips)
library(phangorn)
setwd("your_working_dir")
x <- read.fas("my_aligned_fasta.fasta")
x <- as.phyDat(x)
y <- dist.ml(x, whatever you need)
Yes. To compare distances they must be aligned.
ClustalO can output a distance matrix (--distmat-out=<file> option).
You can try the DIAMOND aligner: https://github.com/bbuchfink/diamond
If all you want is a distance matrix, why bother aligning at all? Try http://spaced.gobics.de/ for amino acids.
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