Tag: Variation

vtools 3.0.4 – Annotate, Summarize and Analyze Next-gen Sequencing Variation data

vtools 3.0.4

:: DESCRIPTION

vtools (variant tools) is a set of tools for annotating and tracking sequence variation for large-scale exome sequencing projects. Unlike some other tools used for Next-Gen sequencing analysis, variant tools is project based and provide a whole set of tools to manipulate and analyze genetic variants.

::DEVELOPER

paul scheet lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • C++ compiler
  • Python

:: DOWNLOAD

 vtools

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 1;28(3):421-2. Epub 2011 Dec 2.
Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools.
San Lucas FA, Wang G, Scheet P, Peng B.

SimFluVar 1.3 – Simulation Tool for Influenza Virus Variation

SimFluVar 1.3

:: DESCRIPTION

SimFluVar is series in SimFlu Computational simulation platform that predict evolutionary pattern of influenza virus.

::DEVELOPER

KISTI & LCBB (Laboratory of Computational Biology & Bioinformatics, SNU)

:: SCREENSHOTS

SimFluVar

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SimFluVar

:: MORE INFORMATION

Citation

A Visualization Tool for Calculating the Genetic Substitution Patterns Between Two Different Groups.
Ahn I, Jang JH, Kim HY, Lee JH, Son HS.
Evol Bioinform Online. 2015 Jul 27;11:179-83. doi: 10.4137/EBO.S28844.

GZ-gamma – Estimate Parameter of Substitution Rate Variation among Sites

GZ-gamma

:: DESCRIPTION

GZ-gamma is designed to estimate the expected number of substitutions of each amino acid (nucleotide) site, and the gamma shape parameter for the rate variation among sites, using a combination of ancestral sequence inference and maximum likelihood estimation when the phylogenetic relationships of these homologous sequences are known.

::DEVELOPER

Jianzhi Zhang ,  Xun Gu 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  GZ-gamma

:: MORE INFORMATION

Citation:

Gu, X. and J. Zhang J (1997)
A simple method for estimating the parameter of substitution rate variation among sites.
Mol. Biol. Evol. 14:1106-1113

GMM – Detects Copy Number Variation from the Distribution of Copy Number Ratios

GMM

:: DESCRIPTION

GMM (Gaussian Mixture Model) detects copy number variation from the distribution of copy number ratios. From the data, it will fit one component for each of the following copy number states: deletion, copy-neutral, 1 and 2 additional copy; with a constraint on the difference between the mixture means. Then for a given individual, it will determine the probabilities for each copy number state and compute the expected copy number (dosage).

::DEVELOPER

Computational Biology Group ,Department of Medical Genetics, University of Lausanne

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  GMM

:: MORE INFORMATION

MoDIL 1.1 – Detect INDEL Variation with Clone-end Sequencing

MoDIL 1.1

:: DESCRIPTION

MoDIL (Mixture of Distributions Indel Locator) is a novel method for finding medium sized indels from high throughput sequencing datasets.

::DEVELOPER

the Computational Biology Labat the University of Toronto’s Department of Computer Science.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MoDIL

:: MORE INFORMATION

Citation

Seunghak Lee, Fereydoun Hormozdiari, Can Alkan & Michael Brudno
MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions
Nature Methods 6, 473 – 474 (2009)

CopyMap 0.813 – Localization of Copy Number Variation

CopyMap 0.813

:: DESCRIPTION

CopyMap is a hidden Markov algorithm to infer copy number variation from a sample of hybridization intensities. The program combines the information across individuals by estimating a transition matrix between every pair of markers using a Baum‐Welch algorithm. The algorithm consists of two steps, the first step estimates the underlying parameters, the second step estimates carrier status in each individual based on the estimated parameters

::DEVELOPER

Sebastian Zöllner @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C Complier

:: DOWNLOAD

  CopyMap

:: MORE INFORMATION

Citation

Sebastian Zöllner
CopyMap: localization and calling of copy number variation by joint analysis of hybridization data from multiple individuals.
Bioinformatics (Oxford, England) 2010;26(21):2776-7.

MANVa 0.982b – Multilocus Analysis of Nucleotide Variation

MANVa 0.982b

:: DESCRIPTION

MANVa (Multilocus Analysis of Nucleotide Variation) is designed to:

  1. Analyze empirical data from a single population and an outgroup species (if included). It is designed for analyzing a large number of independent loci.
  2. Subset of regions can be analyzed (synonymous, silent, introns, etc). A GFF file associated to each alignment can be provided.
  3. Perform multilocus coalescent simulations
  4. Calculate the levels of variation by maximum likelihood for the multilocus set.
  5. Do multilocus analyses: calculate probabilities and confidence intervals for the observed data when comparing with simulated data, and calculate percentiles for simulated data.

::DEVELOPER

Molecular Evolutionary Genetics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

MANVa

:: MORE INFORMATION

This program is distributed under the GNU General Public License:

GNU_GPL_License.txt

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