CHIAMANTE 1.0.3 – Joint Genotype Calling algorithm for Array and Sequence data

CHIAMANTE 1.0.3

:: DESCRIPTION

Chiamante is a genotype caller for Illumina Beadchips that can augment microarray data with genotype likelihoods from sequence data for improved genotype accuracy and call rate. Whilst primarily designed to call genotypes via fusing these two sources of information, Chiamante also functions as a highly accurate array-only caller.

::DEVELOPER

Jared O’Connell and Jonathan Marchini.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CHIAMANTE

:: MORE INFORMATION

Citation

J O’Connell, J. Marchini (2012)
Joint Genotype Calling With Array and Sequence Data.
Genetic Epidemiology. 10.1002/gepi.21657

cnvHap 1.033 – Joint Copy Number Genotyping

cnvHap 1.033

:: DESCRIPTION

cnvHap is a program for joint copy number genotyping, which uses a haplotype model of copy number variation and integrates data from multiple platforms. It also carries out CN association.

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 cnvHap

:: MORE INFORMATION

Citation

Nat Methods. 2010 Jul;7(7):541-6. Epub 2010 May 30.
cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVs.
Coin LJ, Asher JE, Walters RG, Moustafa JS, de Smith AJ, Sladek R, Balding DJ, Froguel P, Blakemore AI.

RactIP 1.2.1 – Joint Secondary Structure Prediction

RactIP 1.2.1

:: DESCRIPTION

RactIP provides services for predicting RNA joint secondary structures under the general type of interaction including kissing hairpins. RactIP runs fast and predicts the maximum expected accuracy (MEA) structure using integer programming (IP) with threshold cut.  RactIP can integrate approximate information on an ensemble of equilibrium joint structures into the objective function of integer programming using posterior internal and external base-paring probabilities.

::DEVELOPER

Yuki KatoKengo Sato.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 RactIP

:: MORE INFORMATION

Citation

Y. Kato, K. Sato, K. Asai and T. Akutsu,
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming,
Nucleic Acids Res., 40, W29-W34, 2012

Y. Kato, K. Sato, M. Hamada, Y. Watanabe, K. Asai and T. Akutsu,
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming,
Bioinformatics, vol. 26, no. 18, pp. i460-i466, 2010.

Spectrum – Joint Bayesian Inference of Population Structure and Recombination Events

Spectrum

:: DESCRIPTION

Spectrum is a program for jointly inferring population structure and recombination events using multi-locus SNP haplotypes. Assuming a number of founder chromosomes, it infers the association of each individual with founders and generates an ancestral spectrum, which displays genetic population structure and reveals details of the genetic diversity of each individual with respect to recovered founder chromosomes. It also estimates empirical recombination rates and hotspots jointly with the population structure.

::DEVELOPER

the SAILING lab (the Laboratory of Statistical Artificial InteLligence and INtegrative Genomics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 Spectrum

:: MORE INFORMATION

Citation

Kyung-Ah Sohn and Eric P. Xing,
Spectrum:Joint Bayesian Inference of Population Structure and Recombination Events.
Bioinformatics. 2007 Jul 1;23(13):i479-89.