EXPANDS 2.1.2 – Expanding Ploidy and Allele-Frequency on Nested Subpopulations

EXPANDS 2.1.2

:: DESCRIPTION

EXPANDS characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux
  • R

:: DOWNLOAD

EXPANDS

:: MORE INFORMATION

Citation

Andor, N., Harness, J. V., Müller, S., Mewes, H. W. & Petritsch, C.
EXPANDS: expanding ploidy and allele frequency on nested subpopulations.
Bioinforma. Oxf. Engl. 30, 50–60 (2014).

KimTree 2.0.1 – Inferring Population Histories using Genome-wide Allele Frequency data

KimTree 2.0.1

:: DESCRIPTION

KimTree is a program aimed at estimating divergence times on a diffusion time scale from large single nucleotide polymorphism (SNP) data

::DEVELOPER

KimTree team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KimTree

:: MORE INFORMATION

Citation

Gautier M and Vitalis R (2013)
Inferring population histories using genome-wide allele frequency data.
Molecular Biology and Evolution 30: 654-668

EM-SNP – Allele Frequency Estimation, SNP Detection and Association Studies

EM-SNP

:: DESCRIPTION

EM-SNP is an unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R

:: DOWNLOAD

  EM-SNP

:: MORE INFORMATION

Citation

Quan Chen and Fengzhu Sun (2013):
A unified approach for allele frequency estimation, SNP detection and association studies on pooled sequencing data using EM algorithms.
BMC Genomics. 2013;14 Suppl 1:S1. doi: 10.1186/1471-2164-14-S1-S1.

iAdmix 0.2 – Using population allele frequencies for Computing Individual Admixture Estimates

iAdmix 0.2

:: DESCRIPTION

iAdmix is a program to estimate individual admixture proportions from DNA sequencing experiments (exome sequencing, targeted sequencing, low coverage whole-genome sequencing or genotyping)

::DEVELOPER

Vikas Bansal, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

 iAdmix

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Jan 16;16(1):4.
Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations.
Bansal V, Libiger O.

Psafe 20120530 – Pooled Sequencing Allele Frequency Estimation

Psafe 20120530

:: DESCRIPTION

Psafe is a pipeline to adjust the biases and errors of sequencing data to gain more accurate allele frequency estimation.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/MacOsX
  • Perl

:: DOWNLOAD

 Psafe

:: MORE INFORMATION

Citation

Genet Epidemiol. 2012 Sep;36(6):549-60. doi: 10.1002/gepi.21648. Epub 2012 Jun 6.
Biases and errors on allele frequency estimation and disease association tests of next-generation sequencing of pooled samples.
Chen X, Listman JB, Slack FJ, Gelernter J, Zhao H.

GeneticDistances 20090824 – Calculate common Genetic Distances for Allele Frequency data

GeneticDistances 20090824

:: DESCRIPTION

GeneticDistances is a program for my graduate students that calculates theta, Ds, and Da for genetic data in GENEPOP format

::DEVELOPER

Steven Kalinowski, Ph.D.

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 GeneticDistances

:: MORE INFORMATION

ALOHA 1.2 – Genome-wide Analysis of Allele Frequency

ALOHA 1.2

:: DESCRIPTION

ALOHA (Allele-Frequency/Loss-of-Heterozygosity/Allelic-Imbalance) is a tool for a genome-wide analysis of allele frequency, detection of loss of heterozygosity and identification of allelic imbalance. Moreover, chromosome-wise allele frequency biplots are provided for sample classification, outlier detection and SNP clustering.

::DEVELOPER

Hsin-Chou Yang

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 ALOHA

:: MORE INFORMATION

Citation

Hsin-Chou Yang*, Hsin-Chi Lin, Mei-Chu Huang, Ling-Hui Li, Wen-Harn Pan, Jer-Yuarn Wu, and Yuan-Tsong Chen (2010).
A new analysis tool for individual-level allele frequency for genomic studies.
BMC Genomics 11: 415