JointSNVMix 0.8.0 – Graphical Model to Analyse Sequence Data from Tumour/normal Pairs

JointSNVMix 0.8.0

:: DESCRIPTION

JointSNVMix implements a probabilistic graphical model to analyse sequence data from tumour/normal pairs. The model draws statistical strength by analysing both genome jointly to more accurately classify germline and somatic mutations.The JointSnvMix software package consists of a number of tools for calling somatic mutations in tumour/normal paired NGS data.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

JointSNVMix

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Apr 1;28(7):907-13. doi: 10.1093/bioinformatics/bts053. Epub 2012 Jan 27.
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.
Roth A1, Ding J, Morin R, Crisan A, Ha G, Giuliany R, Bashashati A, Hirst M, Turashvili G, Oloumi A, Marra MA, Aparicio S, Shah SP.

GPMAP – Global Haplotype Partitioning for Maximal Associated SNP Pairs

GPMAP

:: DESCRIPTION

GPMAP has been developed based on the open source code of Haploview (ver. 4.1). Therefore GPMAP basically inherits all Haploview functions plus the global partitioning method

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux
Java

:: DOWNLOAD

GPMAP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Aug 27;10:269. doi: 10.1186/1471-2105-10-269.
Global haplotype partitioning for maximal associated SNP pairs.
Katanforoush A1, Sadeghi M, Pezeshk H, Elahi E.

DesignPrimer – Design PCR Primer Pairs for the SciRoKo output using Primer3

DesignPrimer

:: DESCRIPTION

The perl script DesignPrimer can be used to design PCR primer pairs for the SciRoKo output using Primer3. An output file is generated that can be directly sent to a company for primer synthesis.

::DEVELOPER

Robert Kofler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows / MacOsX
Perl

:: DOWNLOAD

DesignPrimer

:: MORE INFORMATION

MEDUSA – Selection and Visual Assessment of PCR Primer Pair

MEDUSA

:: DESCRIPTION

MEDUSA is a tool for automatic selection and visual assessment of PCR primer pairs, developed to assist large scale gene expression analysis projects.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Python

MEDUSA

:: MORE INFORMATION

Citation

Bioinformatics. 2001 Jul;17(7):656-7.
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.
Podowski RM, Sonnhammer EL.

RELPAIR 2.0.1 – Relationship of Pairs of Individuals based on Genetic Marker Data

RELPAIR 2.0.1

:: DESCRIPTION

RELPAIR is a FORTRAN 77 program that infers the relationships of pairs of individuals based on genetic marker data, either within families or across an entire sample.

::DEVELOPER

the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX / Windows
FORTRAN

:: DOWNLOAD

RELPAIR

:: MORE INFORMATION

Citation

Epstein, M.P., Duren, W.L., and Boehnke, M. (2000)
Improved inference of relationships for pairs of individuals.
American Journal of Human Genetics 67:1219-1231.