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
window/word size
number of "wildcards"
directory to store unmerged files in. This has to be as least as large as you expect your output matrix to be.
filename to save the output matrix as. Defaults to file.matrix
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.
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