BEDASSLE 1.5 – Bayesian Estimation of Differentiation in Alleles by Spatial Structure and Local Ecology

BEDASSLE 1.5

:: DESCRIPTION

BEDASSLE estimates the relative contributions of pairwise geographic distance and pairwise ecological distance to patterns of genetic variation.

::DEVELOPER

the Bradburd Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BEDASSLE

:: MORE INFORMATION

Citation

Evolution. 2013 Nov;67(11):3258-73. doi: 10.1111/evo.12193.
Disentangling the effects of geographic and ecological isolation on genetic differentiation.
Bradburd GS, Ralph PL, Coop GM.

IBDseq – Detect IBD Segments using Allele Frequencies

IBDseq

:: DESCRIPTION

IBDseq is a software program for detecting segments of identity-by-descent (IBD) and homozygosity-by-descent (HBD) in unphased genetic sequence data.

::DEVELOPER

Brian L. Browning 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

IBDseq

:: MORE INFORMATION

Citation:

Browning BL, Browning SR.
Detecting identity by descent and estimating genotype error rates in sequence data.
Am J Hum Genet. 2013 Nov 7;93(5):840-51. doi: 10.1016/j.ajhg.2013.09.014. Epub 2013 Oct 24. PMID: 24207118; PMCID: PMC3824133.

MULTIPRED2 – large-scale Screening of allele-, genotype-, and supertype-specific HLA Associated Peptides

MULTIPRED2

:: DESCRIPTION

MULTIPRED2 is a computational system for large-scale screening of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR supertypes as well as to alleles belonging to an individual’s genotype.

::DEVELOPER

MULTIPRED2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

J Immunol Methods. 2011 Nov 30;374(1-2):53-61. doi: 10.1016/j.jim.2010.11.009. Epub 2010 Dec 2.
MULTIPRED2: a computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles.
Zhang GL1, DeLuca DS, Keskin DB, Chitkushev L, Zlateva T, Lund O, Reinherz EL, Brusic V.

iConvert – Convert Genotype Allele Formats

iConvert

:: DESCRIPTION

The iConvert program allows to convert genotype allele formats (any format for any SNP chip contained in the SNPchiMp tool).

::DEVELOPER

iConvert team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • Python

:: DOWNLOAD

 iConvert

:: MORE INFORMATION

Citation

SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species.
Nicolazzi EL, Caprera A, Nazzicari N, Cozzi P, Strozzi F, Lawley C, Pirani A, Soans C, Brew F, Jorjani H, Evans G, Simpson B, Tosser-Klopp G, Brauning R, Williams JL, Stella A.
BMC Genomics. 2015 Apr 10;16(1):283.

ABC 1.3 – Allele-specific Binding from ChIP-Seq

ABC 1.3

:: DESCRIPTION

ABC is a computational tool that identifies allele specific binding of transcription factors from aligned ChIP-Seq reads at heterozygous SNVs.

::DEVELOPER

The Computational Biology and Medicine Program (CBMP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ABC

:: MORE INFORMATION

Citation

ABC: A tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.
Bailey SD, Virtanen C, Haibe-Kains B, Lupien M.
Bioinformatics. 2015 May 20. pii: btv321.

Tandem2 – Automated Microsatellite Allele Binning for Population Genetics Workflows

Tandem2

:: DESCRIPTION

All microsatellite analysis software expects allele sizes given in integer numbers, while allele scoring produces allele sizes with two decimals that are dependent not only on fragment length, but also on fluorescent dye, and GC content. Therefore, allele binning is not a trivial task. Tandem2 fills a gap of the microsatellite workflow by rounding allele sizes to valid integers, depending on the microsatellite repeat units.

::DEVELOPER

EVOINFORMATICS GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 Tandem2

:: MORE INFORMATION

Citation

Matschiner M, Salzburger W (2009)
TANDEM: integrating automated allele binning into genetics and genomics workflows.
Bioinformatics, 25(15), 1982-1983.

ASCAT 2.5.2 – Allele-Specific Copy number Analysis of Tumours

ASCAT 2.5.2

:: DESCRIPTION

ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy.

::DEVELOPER

Peter Van Loo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 ASCAT

:: MORE INFORMATION

Citation:

Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16910-5. doi: 10.1073/pnas.1009843107. Epub 2010 Sep 13.
Allele-specific copy number analysis of tumors.
Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, Perou CM, Børresen-Dale AL, Kristensen VN.

cisASE – Detecting Putative Cis-regulated Allele-specific Expression in RNA Sequencing data

cisASE

:: DESCRIPTION

cisASE is a likelihood-based method for ASE detection at multiple levels(SNV,exon and gene). It takes matched DNA sequencing data as reference to reduce artifacts from technical bias and copy number variation to identify ASE due to cis-acting elements, and it works almost as well for dataset without DNA sequencing.

::DEVELOPER

cisASE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R

:: DOWNLOAD

 cisASE

:: MORE INFORMATION

Citation

cisASE: A likelihood-based method for detecting putative cis-regulated allele-specific expression in RNA sequencing data.
Liu Z, Gui T, Wang Z, Li H, Fu Y, Dong X, Li Y.
Bioinformatics. 2016 Jul 13. pii: btw416.

ESTminer 0.3 – Gene and Allele Identification

ESTminer 0.3

:: DESCRIPTION

ESTminer is a collection of programs that use expressed sequence tag (EST) data from inbred genomes to identify unique genes within gene families.

::DEVELOPER

Rex Nelson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX /Windows
  • Perl

:: DOWNLOAD

 ESTminer

:: MORE INFORMATION

Citation

ESTminer: a suite of programs for gene and allele identification.
Nelson RT, Grant D, Shoemaker RC.
Bioinformatics. 2005 Mar 1;21(5):691-3.

LAPD – Estimate Maximum Likelihood Allele and two-locus Haplotype Frequencies

LAPD

:: DESCRIPTION

LAPD (Linkage Analysis Using Pedigree Data) allows to estimate maximum likelihood allele and two-locus haplotype frequencies, using an Expectation-Maximization algorithm, taking into account family relationships of the individuals.

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 LAPD

:: MORE INFORMATION

Citation

Excoffier, L. and Slatkin, M. (1998)
Incorporating genotypes of relatives into a test of linkage disequilibrium,
Am. J. Hum. Genet. 162:171-180.

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