SHEAR 1.1.2 – Sample Heterogeneity Estimation and Assembly by Reference

SHEAR 1.1.2

:: DESCRIPTION

SHEAR is a tool for next-generation sequencing data analysis that predicts SVs, accounts for heterogeneous variants by estimating their representative percentages, and generates personal genomic sequences to be used for downstream analysis.

::DEVELOPER

Hwang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SHEAR

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jan 29;15:84. doi: 10.1186/1471-2164-15-84.
SHEAR: sample heterogeneity estimation and assembly by reference.
Landman SR, Hwang TH1, Silverstein KA, Li Y, Dehm SM, Steinbach M, Kumar V.

Homo 1.2 – Surveying and Visualizing Compositional Heterogeneity across Aligned Sequence data

Homo 1.2

:: DESCRIPTION

Homo is a program written to allow its users to check whether aligned nucleotide or amino acid sequences are consistent with evolution under globally stationary, reversible, and homogeneous (SRH) conditions.

::DEVELOPER

CSIRO Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 Homo is available on request from the author (lars.jermiin@csiro.au).

:: MORE INFORMATION

Citation

Jermiin LS, Lovell DR, von Haeseler A. 2015.
Homo: a program for surveying and visualizing compositional heterogeneity across aligned sequence data.
Systematic Biology (In prep.)

BTP 1.0 – Analyzing Intra-tumor Heterogeneity from High-throughput Sequencing data

BTP 1.0

:: DESCRIPTION

BTP (Binary Tree Partition)is a novel combinatorial formulation of the problem of constructing the subpopulations of tumor cells from the variant allele frequencies of somatic mutations.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 BTP

:: MORE INFORMATION

Citation:

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.
Hajirasouliha I, Mahmoody A, Raphael BJ.
Bioinformatics. 2014 Jun 15;30(12):i78-86. doi: 10.1093/bioinformatics/btu284.

MismatchHetMutRate – Perform Mismatch Analyses allowing for Heterogeneity of Mutation Rates

MismatchHetMutRate

:: DESCRIPTION

MismatchHetMutRate is a series of programs to perform mismatch analyses allowing for heterogeneity of mutation rates.

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MismatchHetMutRate

:: MORE INFORMATION

Citation

Schneider, S. and L. Excoffier (1999)
Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites. Application to human mitochondrial DNA.
Genetics 152: 1079-1089.

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.

SeqVis 1.5 – Visualization of Compositional Heterogeneity in Large Alignments of Nucleotides

SeqVis 1.5

:: DESCRIPTION

SeqVis is a stand-alone, platform-independent Java application developed with the aim to facilitate analysis and 3D visualization of compositional heterogeneity in species-rich alignments of nucleotide sequences. Each sequence is represented by a dot in a tetrahedron plot (i.e., an extension of the de Finetti), where the position of the dot depends uniquely on the nucleotide content of that sequence. Sequences that are compositionally different will appear as dots found in different areas within the tetrahedron. SeqVis also allows users to analyse their data set using, for example, the useful matched-pairs test of symmetry (Ababneh et al. 2006)

::DEVELOPER

Lars S. Jermiin

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOs / Linux / Unix
  • Java

:: DOWNLOAD

  SeqVis

:: MORE INFORMATION

Citation:

Ho JWK, Adams CE, Lew JB, Matthews TJ, Ng CC, Shahabi-Sirjani A, Tan LH, Zhao Y, Easteal S, Wilson SR, Jermiin LS (2006).
SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides.
Bioinformatics 22, 2162-2163.