Gepard 1.40 – Calculation of Dotplots even for Large Sequences

Gepard 1.40

:: 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

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: 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

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.

3V 1.3 – Volume Related Calculations

3V 1.3

:: DESCRIPTION

3V (Voss Volume Voxelator) is collection of program for the assessment of volumes in protein files.. These tools include methods for displaying the surface of macromolecules and extracting internal channels.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 3V

:: MORE INFORMATION

Citation:

Neil R. Voss and Mark Gerstein
3V: cavity, channel and cleft volume calculator and extractor
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W555–W562.

EDIBLE 20110705 – Make Phylogenetic Information Calculations

EDIBLE 20110705

:: DESCRIPTION

EDIBLE (Experimental Design and Information By Likelihood Exploration.) is a software to perform likelihood calculations based on Markov process models of nucleotide substitution allied with phylogenetic trees, and from these to compute Fisher information measures under different experimental designs. These calculations can be used to answer questions of optimal experimental design in molecular phylogenetics.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 EDIBLE

:: MORE INFORMATION

Citation:

EDIBLE: experimental design and information calculations in phylogenetics.
Massingham T, Goldman N.
Bioinformatics. 2000 Mar;16(3):294-5.

Ktreedist 1.0 – Calculation of the Minimum Branch Length Distance (K tree score) between Phylogenetic Trees

Ktreedist 1.0

:: DESCRIPTION

Ktreedist is a computer program written in Perl that calculates the minimum branch length distance from one phylogenetic tree to another, providing a measure of the difference in topology and relative branch lengths (shape) between two trees

::DEVELOPER

Castresana Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Perl

:: DOWNLOAD

 Ktreedist

:: MORE INFORMATION

Citation:

Soria-Carrasco, V., Talavera, G., Igea, J., and Castresana, J. (2007).
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees.
Bioinformatics 23, 2954-2956.

SGFSC – Speeding Gene Functional Similarity Calculation

SGFSC

:: DESCRIPTION

SGFSC is a novel Speeding Gene Functional Similarity Calculation tool

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2016 Nov 4;17(1):445.
SGFSC: speeding the gene functional similarity calculation based on hash tables.
Tian Z, Wang C, Guo M, Liu X, Teng Z

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.

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.