BrpAln sources are written in c++ and one python script to output the alignment file stockholm format.
Unzip:
tar -zxvf BrpAli.tar.gz
Build BrpAli.cpp:
g++ -O3 BrpAli.cpp -o BrpAli
Execute:
./BrpAli [options]
Linux operation system.
g++ compiler.
Python 2.7 and biopython.
-m Match score.
-u Mismatch score.
-g Gap score.
-s Sum of pairs weight in the 3-D alignment.
-i Input file in fasta format.
-o Output file.
-f Output alignment format <sto/fas> for stockholm or fasta