Noisy

Noisy on XSEDE

Noisy is a program to identify problematic columns in multiple sequence alignments. 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++.

Manual for Noisy: http://www.bioinf.uni-leipzig.de/Software/noisy/noisy.1.html

Noisy home page here.

INPUT = dna or protein matrices in aligned fasta format

Simple Example of Run Input/Output

Input File Type	File Name
input file	infile.afa
Output File Type	File Name
log file	output.eps

Known Issues:

• MrBayes 3.2.2 runs with BEAGLE fail quickly with a few data sets. The cause is presently unknown, but it is related to the interaction between MrBayes and BEAGLE. To fix this, clone the failed job, uncheck the "Run Using Beagle" box, and resubmit. These runs will always succeed without BEAGLE, with a slight (20%) run time penalty.

If you use Noisy, 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

If there is a tool or a feature you need, please let us know.