$ g++ -O3 -std=c++0x -o gremlin_cpp gremlin_cpp.cpp -fopenmpinvoke -fopenmp to allow usage of multiple CPU(s), the code is openmp friendly.
Note, openmp uses the system variable OMP_NUM_THREADS to decide how many threads/CPU(s) to use.
$ export OMP_NUM_THREADS=16
$ ./gremlin_cpp -i alignment_file -o results
# ---------------------------------------------------------------------------------------------
# GREMLIN_CPP v1.0
# ---------------------------------------------------------------------------------------------
# -i input alignment (either one sequence per line or in fasta format)
# -o save output to
# ---------------------------------------------------------------------------------------------
# Optional settings
# ---------------------------------------------------------------------------------------------
# -only_neff only compute neff (effective num of seqs) [Default=0]
# -only_v only compute v (1body-term) [Default=0]
# -gap_cutoff remove positions with > X fraction gaps [Default=0.5]
# -alphabet select: [protein|rna|binary] [Default=protein]
# -eff_cutoff seq id cutoff for downweighting similar seqs [Default=0.8]
# -lambda L2 regularization weight [Default=0.01]
# -mrf_i load MRF
# -mrf_o save MRF
# -pair_i load list of residue pairs (one pair per line, index 0)
# ---------------------------------------------------------------------------------------------
# Minimizer settings
# ---------------------------------------------------------------------------------------------
# -min_type select: [lbgfs|cg|none] [Default=lbfgs]
# -max_iter number of iterations [Default=100]
# ---------------------------------------------------------------------------------------------
i j raw apc ii jj
i = index i
j = index j
raw = l2norm(W)
apc = raw - mean(row) * mean(col) / mean(all)
ii = char-position i
jj = char-position j
The out MRF contains 21 values for each position (V) and 21 x 21 values for each pair of positions (W).
The order of the values is as follows: "ARNDCQEGHILKMFPSTWYV-" (where "-" is the gap).
For RNA the order is "AUCG-", with 5 values for V and 5x5 for W.
For Binary the order is "01-", with 3 values for V and 3x3 for W.