WhopGenome 0.9.7 – High-speed Access to Whole-genome Variation Data

WhopGenome 0.9.7

:: DESCRIPTION

WhopGenome is a package for R that provides high-speed access to Variant Call Format (VCF) files as e.g. published by the 1000 Genomes Project.. It also reads in alignments from FASTA, Phylip, MAF and other file formats. Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.

::DEVELOPER

Computational Cell Biology,   Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows  / MacOsX
  • R

:: DOWNLOAD

 WhopGenome

:: MORE INFORMATION

Citation

WhopGenome: high-speed access to whole genome variation and sequence data in R.
Wittelsbürger U, Pfeifer B, Lercher MJ.
Bioinformatics. 2015 Feb 1;31(3):413-5. doi: 10.1093/bioinformatics/btu636

RNAv – Search Genomes for RNA Secondary Structure Variation

RNAv

:: DESCRIPTION

RNAv (RNA secondary structure variation) is a program that searches for RNA secondary structure variations based on the notion of a structure graph to specify the consensus structure of an RNA family.The model for profiling the consensus structure of an RNA family is a conformational graph that specifies the topology of the consensus fold and relationship among helices and unpaired loops. Individual helices and loops are modeled with a restricted Covariance Model and profile HMM, respectively. The fold topology, helices, and loops are trained with an input pasta file that contains a multiple structural alignment for a set of training RNA sequences.

::DEVELOPER

The RNA-Informatics Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Complier

:: DOWNLOAD

 RNAv

:: MORE INFORMATION

Citation

Huang, Z., Malmberg, R., Mohebbi M., and Cai, L. (2010)
RNAv: Non-coding RNA Secondary Structure Variation Search via Graph Homomorphism
Proceedings of Computational Systems Bioinformatics Conference (CSB 2010), August, 2010. Vol. 9, p. 56-69.

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.

PyLOH 1.4.3 – Discovering Copy Number Variations in Cancer Genomes

PyLOH 1.4.3

:: DESCRIPTION

PyLOH is a tool for discovering copy number variations in cancer genomes

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python

:: DOWNLOAD

  PyLOH

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 21.
Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.
Li Y1, Xie X.

CNVphaser / CNVphaserPro 1.1 – Infer CNV Haplotypes with Variations

CNVphaser / CNVphaserPro 1.1

:: DESCRIPTION

CNVphaser infers haplotypes with variations in both copy numbers and nucleotide sequences within a CNV region

CNVphaserPro, a successor of CNVphaser and MOCSphaser to handle noisy CNV data such as microarray data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 CNVphaser / CNVphaserPro

:: MORE INFORMATION

Citation

Am J Hum Genet. 2008 Aug;83(2):157-69. doi: 10.1016/j.ajhg.2008.06.021. Epub 2008 Jul 17.
An algorithm for inferring complex haplotypes in a region of copy-number variation.
Kato M1, Nakamura Y, Tsunoda T.

CONAN 1.1.0 – Copy Number Variation Analysis Software

CONAN 1.1.0

:: DESCRIPTION

CONAN is a freely available client-server software solution which provides an intuitive graphical user interface for categorizing, analyzing and associating CNVs with phenotypes.

::DEVELOPER

GenEpi – Division of Genetic Epidemiology Innsbruck

:: SCREENSHOTS

CONAN

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

 CONAN

:: MORE INFORMATION

Citation

CONAN: copy number variation analysis software for genome-wide association studies.
Forer L, Schönherr S, Weissensteiner H, Haider F, Kluckner T, Gieger C, Wichmann HE, Specht G, Kronenberg F, Kloss-Brandstätter A.
BMC Bioinformatics. 2010 Jun 14;11:318. doi: 10.1186/1471-2105-11-318.

TrioCNV 0.1.2 – Joint Detection of Copy Number Variations in Parent-offspring Trios

TrioCNV 0.1.2

:: DESCRIPTION

TrioCNV is a tool designed to jointly detecting CNVs from WGS data in parent-offspring trios.

::DEVELOPER

yzhuangliu@gmail.com

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R
  • JRE

:: DOWNLOAD

 TrioCNV

:: MORE INFORMATION

Citation

Joint detection of copy number variations in parent-offspring trios.
Liu Y, Liu J, Lu J, Peng J, Juan L, Zhu X, Li B, Wang Y.
Bioinformatics. 2015 Dec 7. pii: btv707.

SHiAT 1.1 – Generates Plots of Variation along Sequence Alignment

SHiAT 1.1

:: DESCRIPTION

SHiAT (Shannon Heterogeneity in Alignments Tool) provides an intuitive graphical interface for the simultaneous calculation of three measures of sitewise variation in DNA or RNA alignments. The Shannon Information index, Hamming distance and (1-consensus frequency) are all calculated and displayed in a series of graphical plots. Multiple alignments may be imported and compared, and a data view panel allows easy copy-and-pasting into external applications.

::DEVELOPER

Joe Parker

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

SHiAT

:: MORE INFORMATION

FEATnotator 1.1.2 – Annotation of Sequence Features and Variation, Facilitating Interpretation in Genomics Experiments

FEATnotator 1.1.2

:: DESCRIPTION

FEATnotator is a light weight, fast and easy to use, open source software program that annotates different kinds of next generation analysis data based on known reference genome annotation information.

::DEVELOPER

FEATnotator team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • R

:: DOWNLOAD

 FEATnotator

:: MORE INFORMATION

Citation:

FEATnotator: A Tool for Integrated Annotation of Sequence Features and Variation, Facilitating Interpretation in Genomics Experiments.
Podicheti R, Mockaitis K.
Methods. 2015 Apr 28. pii: S1046-2023(15)00175-9. doi: 10.1016/j.ymeth.2015.04.028