The purpos of wassermandli is to compare different genes and identify possible gene duplications, pseudogenes of member of same gene families. No a priori knowledge is needed or used.
wassermandli computes all pairwise alignments of a list of genes. The alignments are performed with the Smith Waterman algorithm implemented in water from the EMBOSS package.
wassermandli requires a list of genes of interest and a multifasta file containing the gene sequences (both DNA or AA are possible). By default the results appear as STDOUT, but they can be redirected with "> results.txt". Furthermore all alignments are also saved to an ad hoc created folder WATER_align.
bash wassermandli.sh -h