PRANK: Probabilistic Alignment Kit

PRANK is a probabilistic multiple alignment program for DNA, codon and
amino-acid sequences. It is based on a novel algorithm that treats
insertions correctly and avoids over-estimation of the number of
deletion events.

In addition, PRANK borrows ideas from maximum likelihood (ML) methods
used in phylogenetics and correctly takes into account the evolutionary
distances between sequences.

Lastly, PRANK allows for defining a potential structure for sequences to
be aligned and then, simultaneously with the alignment, predicts the
locations of structural units in the sequences.

NOTE!
The dependencies listed in the REQUIRED field are not needed for
building PRANK. They are, however, highly recommended for the complete
functionality of the program:

1) Progressive alignment requires a guide tree. If no tree is provided,
PRANK constructs one by calling MAFFT to make a quick alignment and
infers an NJ tree from the evolutionary distances based on that.

2) The standard PRANK algorithm is based on an exhaustive search of the
best pairwise solution. PRANK uses Exonerate to anchor the pairwise
alignments and thus speed up the process.

3) To improve the ancestral reconstruction, PRANK uses BppAncestor from
the BppSuite.

NOTE 2: This will not build on a 32bit system.