aacode3 — Produce a weighted matrix from a FASTA filex


aacode [ [-l [-i [-e-b]]] ] [ -w # ] [ -d # ] [ -t tmpdir ] [ -m output_matrix ] [ -p output_pinfo ] {file.txt}


aacode3 takes as input a FASTA file of protein sequences. It will output a matrix of word weights based on the weighting scheme selected. Additionally, it produces a .pinfo file that maps the protein IDs to the elements of the matrix.

aacode3 uses a wordsize to generate the output matrix. When the -d option is specified, this wordsize becomes a window size, and the wordsize is (window-wildcards).



use LBA weighting


use IPF weighting


use log-entropy weights


use binary weights

-w #

window/word size

-d #

number of "wildcards"

-t tmpdir

directory to store unmerged files in. This has to be as least as large as you expect your output matrix to be.

-m output_matrix

filename to save the output matrix as. Defaults to file.matrix

-p output_pinfo

filename to save the output pinfo as. Defaults to file.pinfo


The input FASTA file. This argument is required, and must have a .txt extenstion.