FUGUE 0.2.3 – Haplotype Frequency Estimation

FUGUE 0.2.3

:: DESCRIPTION

FUGUE is the program used to construct haplotypes for the chromosome and linkage disequilibrium maps.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • MERLIN

:: DOWNLOAD

FUGUE

:: MORE INFORMATION

Citation:

Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR and Dunham I
A first-generation linkage disequilibrium map of human chromosome
Nature (2002) 418:544-548

Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, Ankener WM, Alfisi SV, Kuo FS, Camisa AL, Pazorov V, Scott KE, Carey BJ, Faith J, Katari G, Bhatti HA, Cyr JM, Derohannessian V, Elosua C, Forman AM, Grecco NM, Hock CR, Kuebler JM, Lathrop JA, Mockler MA, Nachtman EP, Restine SL, Varde SA, Hozza MJ, Gelfand CA, Broxholme J, Abecasis GR, Boyce-Jacino MT and Cardon LR
Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots.
Nat Genet (2003) 33:382-7

PEDSTATS 0.6.12 – Statistics & Quality Assessments for Gene-mapping Data

PEDSTATS 0.6.12

:: DESCRIPTION

PEDSTATS is a handy tool for quick validation and summary of any pair of pedigree (.ped) and data (.dat) files.PEDSTATS produces summary statistics and basic quality assessments for gene-mapping data, accommodating either pedigree or case-control datasets.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

PEDSTATS

:: MORE INFORMATION

Citation:

Wigginton JE and Abecasis GR (2005)
PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data
Bioinformatics 21:3445 – 3447.

If you decide to use PEDSTATS, please take a minute to register.

SNP-HWE – Routines for exact SNP tests of Hardy-Weinberg Equilibrium

SNP-HWE

:: DESCRIPTION

SNP-HWE (SNP tests of Hardy-Weinberg Equilibrium) is based on an efficient algorithm for enumerating the exact heterozygote probability distribution conditional on the number of minor alleles present in the sample. It adequately controls Type I error rates within large and small samples and is suitable for use in large-scale studies of SNP data. With appropriate citation, these routines are freely available for your use and can be incorporated into other programs.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • C++ Complier

:: DOWNLOAD

SNP-HWE

:: MORE INFORMATION

Citation:

Wigginton JE, Cutler DJ and Abecasis GR
A Note on Exact Tests of Hardy-Weinberg Equilibrium.
Am J Hum Genet (2005) 76: 887-93

If you decide to use SNP-HWE, please take a minute to register.

glfMultiples 20100616 – GLF-based Variant Caller for Next-generation Sequencing data

glfMultiples 20100616

:: DESCRIPTION

glfMultiples is a GLF-based variant caller for next-generation sequencing data. It takes a set of GLF format genotype likelihood files as input and generates a VCF-format set of variant calls as output

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 glfMultiples

:: MORE INFORMATION

GOLD 1.1.0 – Graphical Overview of Linkage Disequilibrium

GOLD 1.1.0

:: DESCRIPTION

GOLD ( Graphical Overview of Linkage Disequilibrium) provides a graphical summary of linkage disequilibrium in human genetic data. The graphical summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. An interface to the Simwalk2 application allows for the analysis of family data.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

GOLD

:: MORE INFORMATION

If you decide to use GOLD, please take a minute to register.

QTDT 2.6.1 – Linkage Disequilibrium Analysis for Quantitative and Discrete Traits

QTDT 2.6.1

:: DESCRIPTION

QTDT (Quantitative and Discrete Traits) provides a convenient one-stop interface for family based tests of linkage disequilibrium. The general models can be used to analyse quantitative or discrete traits in nuclear families, with or without parental genotypes, or extended pedigrees. In addition, QTDT can calculate exact p-values by permutation even when multiple linked polymorphisms are tested.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

QTDT

:: MORE INFORMATION

Citation:

Abecasis GR, Cardon LR and Cookson WO
A General Test of Association for Quantitative Traits in Nuclear Families.
Am J Hum Genet (2000) 66:279-292

Abecasis GR, Cookson WO and Cardon LR
Pedigree tests of transmission disequilibrium.
Eur J Hum Genet (2000) 8:545-51

If you decide to use QTDT, please take a minute to register.

MACH 1.0 – Haplotyping, Genotype Imputation & Disease Association Analysis

MACH 1.0

:: DESCRIPTION

MACH (Markov Chain Haplotyping) is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

MACH

:: MORE INFORMATION

Citation:

Li Y, Willer CJ, Ding J, Scheet P and Abecasis GR (2006)
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes.
Genet Epidemiol 34:816-834.

If you decide to use MACH, please take a minute to register.

ALVIS 0.1 – Explorative Analysis and Visualisation of Multiple Sequence Alignments

ALVIS 0.1

:: DESCRIPTION

Alvis (Interactive non-aggregative multiple sequence ALignment VISualisation) is an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualisation method.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

ALVIS

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2016 May 5;44(8):e77. doi: 10.1093/nar/gkw022.
ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Schwarz RF, Tamuri AU, Kultys M, King J, Godwin J, Florescu AM, Schultz J, Goldman N.

PASSML / Passml_TM – Analysis of Phylogeny / Transmembrane Domain searching from Aligned Amino Acid Sequences

PASSML / Passml_TM

:: DESCRIPTION

PASSML (‘Phylogeny and Secondary Structure using Maximum Likelihood’) has been developed to implement an evolutionary model that combines protein secondary structure and amino acid replacement.

Passml_TM implement an evolutionary model that permits analysis of phylogeny and transmembrane domain searching from aligned amino acid sequences.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PASSML / Passml_TM

:: MORE INFORMATION

Citation

Bioinformatics. 1998;14(8):726-33.
PASSML: combining evolutionary inference and protein secondary structure prediction.
Liò P, Goldman N, Thorne JL, Jones3 DT.

rlsim 1.4 – Simulating RNA-seq library Preparation with Parameter Estimation

rlsim 1.4

:: DESCRIPTION

The rlsim package is a collection of tools for simulating RNA-seq library construction, aiming to reproduce the most important factors which are known to introduce significant biases in the currently used protocols: hexamer priming, PCR amplification and size selection.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Biopython

:: DOWNLOAD

  rlsim

:: MORE INFORMATION

Citation:

Botond Sipos, Tim Massingham and Nick Goldman (2013):
rlsim – a package for simulating RNA-seq library preparation with parameter estimation.
http://bit.ly/rlsim-doc