Information about software packages installed on the ICHEC systems.
PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It's 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 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.
The code is © Ari Löytynoja and distributed under the GPL; an exception are the eigen routines and the sequence input/output functions that come from PAML and readseq packages and are © Ziheng Yang and Don Gilbert, respectively.
To use PRANK, load the relevant environment module:
Further information can be obtained from http://www.ebi.ac.uk/goldman-srv/prank/.
How to cite PRANK:
Löytynoja A. and Goldman N. (2005)
An algorithm for progressive multiple alignment of sequences with insertions.
Proc. Natl. Acad. Sci. USA 102(30): 10557-10562.