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

SelEstim 1.1.7 – Detecting and Measuring Selection from Gene Frequency data

SelEstim 1.1.7

:: DESCRIPTION

SelEstim is a software to detect signatures of selection from gene frequency data and measure the selection intensity

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • R

:: DOWNLOAD

 SelEstim

:: MORE INFORMATION

Citation

Genetics. 2014 Mar;196(3):799-817. doi: 10.1534/genetics.113.152991. Epub 2013 Dec 20.
Detecting and measuring selection from gene frequency data.
Vitalis R1, Gautier M, Dawson KJ, Beaumont MA.

CoNVEM – CNV Allele Frequency Estimation by Expectation Maximisation

CoNVEM

:: DESCRIPTION

CoNVEM (Copy Number Variation Expectation Maximisation) is an expectation-maximization program for determining allelic spectrum from CNV data (CoNVEM)

::DEVELOPER

Bristol Genetic Epidemiology Laboratories at the University of Bristol,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Hum Mutat. 2010 Apr;31(4):414-20. doi: 10.1002/humu.21199.
An expectation-maximization program for determining allelic spectrum from CNV data (CoNVEM): insights into population allelic architecture and its mutational history.
Gaunt TR1, Rodriguez S, Guthrie PA, Day IN.

SFselect – Learning Natural Selection from the Site Frequency Spectrum

SFselect

:: DESCRIPTION

SFselect is a method for classifying genomic regions evolving under positive selection, from those evolving neutrally

::DEVELOPER

Roy Ronen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SFselect

:: MORE INFORMATION

Citation

Genetics. 2013 Sep;195(1):181-93. doi: 10.1534/genetics.113.152587. Epub 2013 Jun 14.
Learning natural selection from the site frequency spectrum.
Ronen R, Udpa N, Halperin E, Bafna V.

d2Tools 20140521 – Counting the Frequency of K-tuple from Sequencing Datasets and calculate the Dissimilarity

d2Tools 20140521

:: DESCRIPTION

d2Tools are the toolbox for counting the frequency of K-tuple from sequencing datasets and then calculating the pairwise dissimilarity matrix between samples with the d2-style (d2/d2*/d2S representing d2/d2Star/d2shepp, respectively) measures

::DEVELOPER

d2Tools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R

:: DOWNLOAD

 d2Tools

:: MORE INFORMATION

Citation

Comparison of metatranscriptomic samples based on k-tuple frequencies.
Wang Y, Liu L, Chen L, Chen T, Sun F.
PLoS One. 2014 Jan 2;9(1):e84348. doi: 10.1371/journal.pone.0084348

Ehapp – Estimate Haplotype Frequency from Pooled Sequencing data

Ehapp

:: DESCRIPTION

Taking advantage of prior haplotype database, Ehapp implements lsqnonneg and GPSR algrithm to estimate the frequencies of haplotypes from pooled sequencing data.

::DEVELOPER

Bioinfomatics Lab of SouthEast Universtity

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Ehapp

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 9. pii: btu670.
Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing.
Cao CC1, Sun X

SLPFA – Subcellular Location Prediction with Frequency and Alignment

SLPFA

:: DESCRIPTION

SLPFA is a predictor for subcellular location prediction of proteins by feature vectors based on amino acid composition (frequency) and sequence alignment. 90.96% of overall accuracy was obtained through fivefold cross validation tests with TargetP plant data sets.

SLPFA is an improved subcellular location predictor of SLP-Local

::DEVELOPER

Akutsu Laboratory (Laboratory of Mathematical Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2007 Nov 30;8:466.
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition.
Tamura T, Akutsu T.

JFreq – Frequencies of Short Nucleotide Sequences

JFreq

:: DESCRIPTION

JFreq (Java Word Frequencies) is a front end to Schbath’s R’MES, which is available at the R’MES website. R’MES finds the expected and actual frequencies of short nucleotide sequences, or words, using a Markov model to control for the effects of base composition and the frequencies of shorter words. Unusually frequent or infrequent occurrences of certain words may indicate biological relevance. For example, if the word “TAATTT” occurs much less frequently than expected, it might be that it performs some regulatory function, or makes the sequence vulnerable to mutation, or has some other biological function.

::DEVELOPER

Dr. Chris Upton, University of Victoria, Biochemistry and Microbiology

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

JFreq

:: MORE INFORMATION

FreClu – Efficient Frequency-based De novo Short Read Clustering

FreClu

:: DESCRIPTION

FreClu: Efficient Frequency-based De novo Short Read Clustering — de novo clustering

::DEVELOPER

Morishita Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java 

:: DOWNLOAD

 FreClu

:: MORE INFORMATION

Citation

Wei Qu, Shin-ichi Hashimoto and Shinichi Morishita
Efficient frequency-based de novo short read clustering for error trimming in next-generation sequencing.
Genome Res. 2009. 19:1309-1315

 

ML-NullFreq 200906 – Estimates the Frequency of Null Alleles at Microsatellite Loci

ML-NullFreq 200906

:: DESCRIPTION

ML-NullFreq  estimates the Frequency of Null Alleles at Microsatellite Loci.

::DEVELOPER

Steven Kalinowski, Ph.D.

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

  ML-NullFreq

:: MORE INFORMATION

Citation

Steven T Kalinowski, Mark L Taper
Maximum likelihood estimation of the frequency of null alleles at microsatellite loci
Conservation Genetics (2006) Volume: 7, Issue: Pages: 991-995