SCANMS 2.02 – Adjusting for multiple Comparisons in sliding window neutrality tests

SCANMS 2.02

:: DESCRIPTION

SCANMS is an open source utility written in Perl that works in conjunction with Richard Hudson’s coalescent simulator MS to do parametric bootstrapping of a sliding window analysis of neutrality test statistics.

::DEVELOPER

Ardell Lab @ UC Merced

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ MacOsX
Perl

:: DOWNLOAD

SCANMS

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Aug 12;20(12):1986-8.
SCANMS: adjusting for multiple comparisons in sliding window neutrality tests.
Ardell DH

cswA 0.01 – Conserved Seq Window Annotater

cswA 0.01

:: DESCRIPTION

cswA reads a .FAS file, along with a set of scores and putative sequence elements and visually annotates the input sequence with the conservation information as well as the position (and match) of the sequence elements.

::DEVELOPER

Dr. Philipp Schlüter

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

cswA

:: MORE INFORMATION

SDSW 0.03 – Sliding Divergence Sequence Window

SDSW 0.03

:: DESCRIPTION

SDSW (Sliding Divergence Sequence Window) needs a set of ALIGNED FASTA format sequences (at least two; gap character ‘-‘) as input and computes pairwise mismatch values for sliding windows of a given size, with a given step size. This is done for every pair of sequences in the input file, and, in addition, average values across all pairs are calculated. Calculations are done in two ways: (a) ignoring comparisons of a nucleotide chararcter with a gap character (N/-) in the mismatch, or (b) including it (more details in the accompanying pdf). The output is written as tab-delimited text.

::DEVELOPER

Dr. Philipp Schlüter

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

SDSW

:: MORE INFORMATION