PALMA aligns two genomic sequences in an optimal way according to its underlying algorithm and trained parameters. The main Python script takes two FASTA files containing the target (e.g. a DNA sequence, part of the genome) and query sequences (e.g. a cDNA or EST sequence).

PALMA creates an alignment using dynamic programming (written in c++), and returns the alignment in a psl like format.

The algorithms will be the ones that will compute optimal local alignments, so if no alignment has been found it is because no alignment got a sufficiently high alignment score.

Requirements:

· Shogun
· Python