PRESTO 1.01 – Calculation of Order Statistic Distributions and Multiple-testing Adjusted P-values via Permutation

PRESTO 1.01

:: DESCRIPTION

PRESTO is optimized software for permutation testing and for computing empirical distributions of order statistics via permutation. PRESTO is extremely fast and can efficiently analyze data from one and two-stage whole genome association studies with millions of markers genotyped on thousands of samples.

::DEVELOPER

Brian L. Browning

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

PRESTO

:: MORE INFORMATION

Citation:

B L Browning (2008)
PRESTO: Rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.
BMC Bioinformatics 9:309.

ROMA – Calculation of Gene Set Activities from Oomics data

ROMA

:: DESCRIPTION

ROMA (Representation and quantification Of Module Activities) is a software package written in Java for the quantification and representation of biological module activity using gene expression or other omics data.

::DEVELOPER

Computational Systems Biology of Cancer group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Java

:: DOWNLOAD

ROMA

:: MORE INFORMATION

Citation:

Martignetti L, Calzone L, Bonnet E, Barillot E, Zinovyev A.
ROMA: Representation and Quantification of Module Activity from Target Expression Data.
Front Genet. 2016 Feb 19;7:18. doi: 10.3389/fgene.2016.00018. PMID: 26925094; PMCID: PMC4760130.

ZygProb – Zygosity Probability Calculation

ZygProb

:: DESCRIPTION

ZygProb processes convenient and accurate zygosity probability calculation.

::DEVELOPER

the Statistical and Genomic Epidemiology Laboratory (SGEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: 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.

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

MicroPattern – Microbe Set Enrichment Analysis and Disease Similarity Calculation

MicroPattern

:: DESCRIPTION

MicroPattern is a tool used to mine regular rules and patterns behind a list of microbes. MicroPattern can also be used to calculate the similarity between the given disease-associated microbe list and the collected micro-disease association dataset

::DEVELOPER

the Cui Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Ma W, Huang C, Zhou Y, Li J, Cui Q.
MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes.
Sci Rep. 2017 Jan 10;7:40200. doi: 10.1038/srep40200. PMID: 28071710; PMCID: PMC5223220.

DelPhi Force – Electrostatic Force Calculation Web Server

DelPhi Force

:: DESCRIPTION

DelphiForce is a DelPhi-based script allowing to calculate electrostatic force between two objects, such as proteins, DNAs, lipids, small molecules, etc.

::DEVELOPER

Professor Emil Alexov Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Li L, Jia Z, Peng Y, Chakravorty A, Sun L, Alexov E.
DelPhiForce web server: electrostatic forces and energy calculations and visualization.
Bioinformatics. 2017 Nov 15;33(22):3661-3663. doi: 10.1093/bioinformatics/btx495. PMID: 29036596; PMCID: PMC5870670.

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.

libScopes 0.1.1 – C++ Library for Calculation of Biochemical Scopes

libScopes 0.1.1

:: 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.

FastPairMI – Fast Calculation of Pairwise Mutual Information Based on Kernel Estimation

FastPairMI

:: DESCRIPTION

FastPairMI is a new software implementation for more efficiently computing the mutual information for all pairs of genes from gene expression microarrays.

::DEVELOPER

Peng Qiu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
MatLab

:: DOWNLOAD

FastPairMI

:: MORE INFORMATION

Citation

Qiu P, Gentles AJ, Plevritis SK.
Fast calculation of pairwise mutual information for gene regulatory network reconstruction.
Comput Methods Programs Biomed. 2009 May;94(2):177-80. doi: 10.1016/j.cmpb.2008.11.003. Epub 2009 Jan 22. PMID: 19167129.

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.