Match 3 alignments together

This tool gives opportunity to find alignments where any other software failed, but user suspects that there are some homology between sequences. Software requires 3 files with alignments. First one, pairwise alignment, must contain 2 sequences, let's call them MASTER1 and MASTER2 that share part of sequences that are homologous. Next two files contain larger alignments with MASTER1 and MASTER2 on the top of them. In this two files homology between MASTER1 and rest of Large alignment #1 and MASTER2 and rest of Large alignment #2 are easier to find than in oppposite situation where we would like to find homology between MASTER1 and Large alignment #2. After uploading files correctly software will merge all sequences into one alignment file.