JMS v1 – Evaluation of Diagnostic Status of Juxtaposed Microsatellite Systems

JMS v1

:: DESCRIPTION

JMS (Juxtaposed microsatellite systems) is a computer program for a simulation-based evaluation of the diagnostic status of juxtaposed microsatellite systems.

::DEVELOPER

Arnaud Estoup

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 JMS

:: MORE INFORMATION

Citation

Estoup A, Cornuet JM, Rousset F, Guyomard R (1999)
Juxtaposed microsatellite systems as diagnostic markers for admixture: theorical aspects.
Molecular Biology and Evolution, 16, 898-908.

EFIN – Evaluation of Functional Impact of Nonsynonymous SNPs

EFIN

:: DESCRIPTION

EFIN is a free tool which predict whether amino acids substitution would related to disease evaluated by random forests based on protein conservation.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICSUniversity of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jun 10;15:455. doi: 10.1186/1471-2164-15-455.
EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome.
Zeng S, Yang J, Chung BH, Lau YL, Yang W

BTEVAL – Evaluation of beta-turn Prediction

BTEVAL

:: DESCRIPTION

The aim of BTEVAL server is to evaluate beta turn prediction algorithms on a uniform data set of 426 proteins or subsets of these proteins. It is the new data set in which no two protein chains have more that 25% sequence identity and each chain contains minimum one beta turn.

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur, H. and Raghava, G.P.S. (2003)
BTEVAL: A server for evaluation of beta-turn prediction methods.
Journal of Bioinformatics and Computational Biology 3(1), 495-504.

TCS – Evaluation and Filtering of multiple Sequence Alignments

TCS

:: DESCRIPTION

TCS (Transitive Consistency Score) web server is a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.
Chang JM, Di Tommaso P, Lefort V, Gascuel O, Notredame C.
Nucleic Acids Res. 2015 Apr 8. pii: gkv310.

TSCAN 1.7.0 – Pseudo-time Reconstruction and Evaluation in Single-cell RNA-seq Analysis

TSCAN 1.7.0

:: DESCRIPTION

TSCAN (Tools for Single-Cell ANalysis) is a software tool developed to better support in silico pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis.

::DEVELOPER

Zhicheng Ji

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 TSCAN

:: MORE INFORMATION

Citation

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.
Ji Z, Ji H.
Nucleic Acids Res. 2016 May 13. pii: gkw430.

MetaReg – Graphical Interface for Modeling and Evaluation of Biological Systems

MetaReg.

:: DESCRIPTION

MetaReg is a Java application aimed to provide the biologist with an intuitive graphical interface for both definition and analysis of system models. The application makes it possible to navigate the model network and compare its predicted and observed behavior.

::DEVELOPER

Prof. Ron Shamir’s Computational Genomics Group at Tel Aviv University.

:: SCREENSHOTS

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MetaReg

:: MORE INFORMATION

Citation

I. Gat-Viks and R. Shamir.
MetaReg application: a graphical interface for modeling and evaluation of biological systems.
Genome Biology (2008) Vol. 9 No. R1

CAD-score 20141216 – Evaluation of Protein Structural Models against the Reference Structure

CAD-score 20141216

:: DESCRIPTION

CAD-score is a new evaluation function quantifying differences between physical contacts in a model and the reference structure.

CAD-score Online Version

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 CAD-score

:: MORE INFORMATION

Citation

CAD-score: A new contact area difference-based function for evaluation of protein structural models.
Olechnovič K, Kulberkytė E, Venclovas C.
Proteins. 2013 Jan;81(1):149-62. doi: 10.1002/prot.24172. Epub 2012 Sep 29.

REAPR 1.0.18 – Genome Assembly Evaluation

REAPR 1.0.18

:: DESCRIPTION

REAPR (Recognising Errors in Assemblies using Paired Reads) is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.

::DEVELOPER

REAPR  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 REAPR

:: MORE INFORMATION

Citation:

REAPR: a universal tool for genome assembly evaluation.
Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD.
Genome Biol. 2013 May 27;14(5):R47

ClustEval – Integrative Clustering Evaluation Framework

ClustEval 1.2

:: DESCRIPTION

ClustEval is a free and extendable opensource platform for objective performance comparison of arbitrary Clustering Methods on different datasets.

::DEVELOPER

ClustEval team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 ClustEval

:: MORE INFORMATION

Citation

Comparing the performance of biomedical clustering methods.
Wiwie C, Baumbach J, Röttger R.
Nat Methods. 2015 Nov;12(11):1033-8. doi: 10.1038/nmeth.3583.

GOPET – Gene Ontology Term Prediction and Evaluation Tool

GOPET

:: DESCRIPTION

GOPET is a complete automated tool for assigning molecular function terms to cDNA or protein sequences utilising Gene Ontology for annotation terms, GO-mapped protein databases for performing homology searches, and Support Vector Machines for the prediction and the assignment of confidence values.

::DEVELOPER

HUSAR Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Mar 20;7:161.
GOPET: a tool for automated predictions of Gene Ontology terms.
Vinayagam A1, del Val C, Schubert F, Eils R, Glatting KH, Suhai S, König R.