NLDMseq – Expression Calculation at both Gene and Isoform levels from RNA-seq data given a Reference Transcriptom

NLDMseq

:: DESCRIPTION

NLDMseq is a bioinformatics tool for expression calculation at both gene and isoform levels from RNA-seq data by considering isoform- and exon-specific read sequencing rate.

::DEVELOPER

Xuejun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

 NLDMseq

:: MORE INFORMATION

Citation

Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.
Liu X, Shi X, Chen C, Zhang L.
BMC Bioinformatics. 2015 Oct 16;16(1):332. doi: 10.1186/s12859-015-0750-6.

Gepard 1.4 – Calculation of Dotplots even for Large Sequences

Gepard 1.4

:: DESCRIPTION

Gepard (German: “cheetah”, Backronym for “GEnome PAir – Rapid Dotter”) allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes.

::DEVELOPER

Institute of Computational Biology, German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java 

:: DOWNLOAD

  Gepard

:: MORE INFORMATION

Citation

Krumsiek J, Arnold R, Rattei T.
Gepard: A rapid and sensitive tool for creating dotplots on genome scale.
Bioinformatics 2007; 23(8): 1026-8. PMID: 17309896

DelPhiPKa – Protonation and pKa Calculation Websever

DelPhiPKa

:: DESCRIPTION

Delphi-PKA is a DelPhi-based C++ program, allowing to predict pKa’s for ionizable groups in proteins, RNA and DNA.

::DEVELOPER

Professor Emil Alexov Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • C COmpiler

:: DOWNLOAD

 DelPhiPKa

:: MORE INFORMATION

Citation

DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs.
Wang L, Zhang M, Alexov E.
Bioinformatics. 2015 Oct 29. pii: btv607.

FastSP 1.6.0 – Calculation of Alignment Accuracy

FastSP 1.6.0

:: DESCRIPTION

FastSP is a Java program for computing alignment error (SP-FN) quickly and using little memory.

::DEVELOPER

The Warnow Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/MacOsX
  • Java

:: DOWNLOAD

  FastSP

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Dec 1;27(23):3250-8. doi: 10.1093/bioinformatics/btr553. Epub 2011 Oct 7.
FastSP: linear time calculation of alignment accuracy.
Mirarab S1, Warnow T.

ZygProb – Zygosity Probability Calculation

ZygProb

:: DESCRIPTION

ZygProb processes convenient and accurate zygosity probability calculation.

::DEVELOPER

Dale R. Nyholt

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Twin Res Hum Genet. 2006 Apr;9(2):194-7.
On the probability of dizygotic twins being concordant for two alleles at multiple polymorphic loci.
Nyholt DR.

NetworkDiversity 1.0.0 – Calculation of beta diversity over Phylogenetic Networks

NetworkDiversity 1.0.0

:: DESCRIPTION

Network Diversity  is a software package for calculating beta diversity over split systems, a widely used class of implicit phylogenetic networks.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows /MacOsX
  • C++ Compiler

:: DOWNLOAD

 Network Diversity

:: MORE INFORMATION

Citation

Mol Biol Evol. 2012 Dec;29(12):3947-58. doi: 10.1093/molbev/mss200.
Measuring community similarity with phylogenetic networks.
Parks DH, Beiko RG.

libScopes – C++ Library for Calculation of Biochemical Scopes

libScopes

:: DESCRIPTION

libScopes can be used to predict the network behavior for metabolic, signaling and gene regulatory networks. The library can calculate biochemical scopes based on give biochemical reaction networks and predefined initial conditions

::DEVELOPER

Theoretical Biophysics Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux
  • C++ Compiler

:: DOWNLOAD

 libScopes 

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 15;28(4):557-63. doi: 10.1093/bioinformatics/btr697. Epub 2011 Dec 22.
Modeling mechanistic biological networks: an advanced Boolean approach.
Handorf T1, Klipp E.

vFitness – Calculation and Estimation in Competitive Virus Fitness

vFitness

:: DESCRIPTION

vFitness is a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments.

::DEVELOPER

vFitness team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 May 18;11:261. doi: 10.1186/1471-2105-11-261.
vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments.
Ma J, Dykes C, Wu T, Huang Y, Demeter L, Wu H.

CofI and Cy2T – Calculation of Coefficients of Inbreeding

CofI and Cy2T

:: DESCRIPTION

CofI and Cy2T calculates coefficients of inbreeding from pedigrees (including extraction of pedigree data from Cyrillic files).

::DEVELOPER

Leeds Institute of Molecular Medicine

:: SCREENSHOTS

CofI

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 CofI and Cy2T

:: MORE INFORMATION

CHEMMOL 1.0 – Calculation of Molecular Masses and Chemical Analysis of Compounds

CHEMMOL 1.0

:: DESCRIPTION

CHEMMOL is a freeware program for the calculation of molecular masses and chemical analyses of compounds. It was written with the organic chemist in mind.

::DEVELOPER

Wolf van Heeswijk

:: SCREENSHOTS

CHEMMOL

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 CHEMMOL

:: MORE INFORMATION