Tag: Frequency

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.

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

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

FOCK 1.0 – Frequency of Oligos

FOCK 1.0

:: DESCRIPTION

FOCK Analyzes a FASTA sequence for n-mer frequency (specified by user). Useful for identifying common or rare restriction sites, etc.

::DEVELOPER

Falkow Lab

:: SCREENSHOTS

Command-line interface.

:: REQUIREMENTS

:: DOWNLOAD

FOCK for Win ; Source Code

:: MORE INFORMATION

The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.