Tag: Polymorphism

HAPAA 1.0 – HMM-based Analysis of Polymorphisms in Admixed Ancestries

HAPAA 1.0

:: DESCRIPTION

HAPAA is a novel approach for ancestry inference that models the allelic and haplotypic variation in the populations and captures the signal of correlation due to linkage disequilibrium, resulting in greatly improved accuracy.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 HAPAA

:: MORE INFORMATION

Citation

Genome Res. 2008 Apr;18(4):676-82. doi: 10.1101/gr.072850.107.
Effect of genetic divergence in identifying ancestral origin using HAPAA.
Sundquist A, Fratkin E, Do CB, Batzoglou S.

TEMP v1.04 – Analyzing Transposable Element Polymorphism in Populations

TEMP v1.04

:: DESCRIPTION

TEMP is a software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data

::DEVELOPER

Zlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TEMP

:: MORE INFORMATION

Citation

TEMP: a computational method for analyzing transposable element polymorphism in populations.
Zhuang J, Wang J, Theurkauf W, Weng Z.
Nucleic Acids Res. 2014 Jun;42(11):6826-38. doi: 10.1093/nar/gku323.

SNiPlay v3 – SNP and Polymorphism Analysis

SNiPlay v3

:: DESCRIPTION

SNiPlay is a web-based tool for SNP and polymorphism analysis.From sequencing traces, alignment or allelic data given as input, it detects SNP and insertion/deletion events.

::DEVELOPER

SNiPlay team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.
Dereeper A, Homa F, Andres G, Sempere G, Sarah G, Hueber Y, Dufayard JF, Ruiz M.
Nucleic Acids Res. 2015 Jun 3. pii: gkv351.

BMC Bioinformatics. 2011 May 5;12:134. doi: 10.1186/1471-2105-12-134.
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.
Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P.

Encore 1.31 – Polymorphism-friendly Error Correction

Encore 1.31

:: DESCRIPTION

Encore is a sequencing error correction tool that is designed for highly polymorphic genome sequencing projects. It can be used as a preprocessing tool for de novo assembly or as a read correction tool for any other purpose. It supports multiple NGS platforms and is suitable for low-polymorphism datasets as well as datasets with high SNP and micro-indel rates.

::DEVELOPER

Nilgun Donmez and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Encore

:: MORE INFORMATION

Citation

Nilgun Donmez and Michael Brudno (2011)
Hapsembler: an assembler for highly polymorphic genomes.
In Proceedings of the 15th Annual international conference on Research in computational molecular biology (RECOMB’11), Springer-Verlag, Berlin, Heidelberg, 38-52.

AnA-FiTS 1.0.3 – Forward-in-time Simulator for Polymorphism data

AnA-FiTS 1.0.3

:: DESCRIPTION

AnA-FiTS is an efficient tool for simulating polymorphism data forward-in-time on the chromosome and genome level.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD 

  AnA-FiTS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Jul 9;14:216. doi: 10.1186/1471-2105-14-216.
Rapid forward-in-time simulation at the chromosome and genome level.
Aberer AJ, Stamatakis A.

maxhap – Estimating Cross-over and Gene Ronversion Rates from Haploid (phased) Polymorphism data

maxhap

:: DESCRIPTION

maxhap is a program for estimating rho (4Nr), a crossing-over parameter, and f (= g/r) a gene conversion parameter using a maximum composite likelihood method

::DEVELOPER

Richard R. Hudson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  maxhap

:: MORE INFORMATION

Citation:

Hudson, R. R. (2001)
Two-locus sampling distributions and their application. 
Genetics 159: 1805-1817

maxdip – Estimating Cross-over and Gene Conversion Rates from Diploid unphased Polymorphism data

maxdip

:: DESCRIPTION

maxdip is a software to estimate rho (4Nr) and gene conversion rates  using random samples with two-site  unphased diploid information. The estimate is obtained by a maximum composite likelihood method based on pairs of sites,

::DEVELOPER

Richard R. Hudson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 maxdip

:: MORE INFORMATION

Citation:

Hudson, R. R. (2001)
Two-locus sampling distributions and their application.
Genetics 159: 1805-1817

DNA Slider – Tests Heterogeneity in the Polymorphism-to-divergence Ratio among Different Regions of a Gene

DNA Slider

:: DESCRIPTION

DNA Slider is program for performing four significance tests of heterogeneity in the ratio of polymorphic sites to fixed differences in DNA sequence data.

::DEVELOPER

John H. McDonald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 DNA Slider

:: MORE INFORMATION

Citation

McDonald, J.H. 1998.
Improved tests for heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence.
Molecular Biology and Evolution 15: 377-384.

MAPP 20050628 – Multivariate Analysis of Protein Polymorphism

MAPP 20050628

:: DESCRIPTION

MAPP (Multivariate Analysis of Protein Polymorphism) considers the physicochemical variation present in a column of a protein sequence alignment and, on the basis of this variation, predicts the impact of all possible amino acid substitutions on the function of the protein.

::DEVELOPER

Sidow Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 MAPP

:: MORE INFORMATION

Citation

Stone EA, Sidow A.
Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
Genome Res. 2005 Jul;15(7):978-86.