academic/prank-msa: Added (probabilistic alignment program).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 32 insertions, 0 deletions

diff --git a/academic/prank-msa/README b/academic/prank-msa/README
new file mode 100644
index 000000000000..4bc1a9f838f1
--- /dev/null
+++ b/academic/prank-msa/README
@@ -0,0 +1,32 @@
+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.