In a first phase the rows of the input multiple sequence alignment (MSA) in
multi fasta format are reordered to conform to a circular ordering. For
this purpose noisy includes the corresponding subset of
routines from David Bryant and Vincent Moulton's NeighborNet
and Stefan Grünewald's QNet packages. Subsequently, a
reliability score for each column of the reordered MSA is
calculated. Essentially, the number of character state alterations in an
alignment column is counted and compared to the observed count in random
shufflings of the column. The uniform pseudo-random number generator
Mersenne Twister is used to generate the random shufflings of alignment
columns.
Noisy exports a PostScript file, visualizing the
quality of the columns of the reordered input MSA, the reliability score of
all columns of the reordered input MSA as xy-data and a
modified alignment in which columns with a reliability smaller then a
cutoff value (set via option --cutoff) are removed. The program noisy is
written in ISO C++.
Noisy's man page.
Download
source code
of program Noisy release 1.5.12
Literature
If you use the program Noisy in your work please cite:
Andreas W. M.Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald,
Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler
Noisy: identification of problematic columns in
multiple sequence alignments.
Algorithms Mol Biol, 3:7 (2008).
doi:10.1186/1748-7188-3-7
Stefan Grünewald, Kristoffer Forslund, Andreas W. M.Dress, Vincent Moulton
QNet: An Agglomerative Method for the Construction of
Phylogenetic Networks from Weighted Quartets.
Mol Biol Evol, 24(2):532-538 (2007).
doi:10.1093/molbev/msl180
David Bryant, Vincent Moulton
Neighbor-Net: An Agglomerative Method for the
Construction of Phylogenetic Networks
Mol Biol Evol, 21(2):255-265 (2004).
doi:10.1093/molbev/msh018s
Contact
Sonja Prohaska
<sonja@bioinf.uni-leipzig.de>