APOLLO – Assess Protein Single or Multiple Model(s)

APOLLO

:: DESCRIPTION

APOLLO pairwise is a program to assess the quality of a pool of structure models predicted for a protein. Teh software evaluates the absolute and/or relative qualities of multiple models or a single model

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 APOLLO

:: MORE INFORMATION

Citation

Zheng Wang, Jesse Eickholt, and Jianlin Cheng, (2011)
APOLLO: A Quality Assessment Service for Single and Multiple Protein Models,
Bioinformatics, 27(12), 1715-1716.

SIRIUS 3.0.3 – Identification of Metabolites using single and Tandem Mass Spectrometry

 Sirius 3.0.3

:: DESCRIPTION

Sirius ,(Sum formula Identification by Ranking Isotope patterns Using mass Spectrometry) a new java-based software framework for discovering a landscape of de-novo identification of metabolites using single and tandem mass spectrometry. Sirius2 deduces molecular formulas of small compounds by ranking isotope patterns from mass spectra of high resolution. Sirius2 further analyses the fragmentation pattern of a compound resulting in hypothetical fragmentation trees. It allows for automated and high-throughput analysis of small-compound MS data beyond elemental composition without requiring compound structures or a mass spectral database.

::DEVELOPER

Lehrstuhl Bioinformatik Jena

:: SCREENSHOTS

SIRIUS

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

   Sirius

:: MORE INFORMATION

Citation:

SIRIUS: decomposing isotope patterns for metabolite identification
Sebastian B?cker, Matthias C. Letzel, Zsuzsanna Lipták and Anton Pervukhin
Bioinformatics (2009) 25 (2): 218-224

Heinz 2.0 / xHeinz 1.0 – Single / Cross-species Module Discovery

Heinz 2.0 /xHeinz 1.0

:: DESCRIPTION

Heinz is a tool for single-species active module discovery.

xHeinz is a software solver that searches for active subnetwork modules that are conserved between two species. It uses a branch-and-cut algorithm that finds provably optimal or near-optimal solutions.

::DEVELOPER

Centrum Wiskunde & Informatica (CWI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

Heinz / xHeinz

:: MORE INFORMATION

Citation

xHeinz: An algorithm for mining cross-species network modules under a flexible conservation model.
El-Kebir M, Soueidan H, Hume T, Beisser D, Dittrich M, Müller T, Blin G, Heringa J, Nikolski M, Wessels LF, Klau GW.
Bioinformatics. 2015 May 27. pii: btv316

SSEdit 6.08 – Single (Short) Sequence Editor

SSEdit 6.08

:: DESCRIPTION

SSEdit is a MacOS X application for viewing and editing single sequences.  Input and output files in FASTA, NRBF, Staden and other formats are supported with the capability to recognise some by the file extension name.

::DEVELOPER

Dr Peter StockwellDepartment of Biochemistry, University of Otago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 SSEdit

:: MORE INFORMATION

PASOS 1.0 – Parental Allocation of Singles in Open Systems

PASOS 1.0

:: DESCRIPTION

PASOS (Parental Allocation of Singles in Open Systems) is “a parental allocation program designed to identify collected parents based on individual multilocus genotypes while detecting missing parents when a proportion of them have not been collected. It makes use of restricted error tolerance in order to distinguish between a partially incorrect genotype from a false parent’s genotype.

:: DEVELOPER

Dr Louis Bernatchez

:: SCREENSHOTS

PASOS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PASOS

:: MORE INFORMATION

Citation

DUCHESNE, P., CASTRIC, T. L. BERNATCHEZ. 2005.
PASOS (parental allocation of singles in open systems): A computer program for individual parental allocation with missing parents.
Molecular Ecology Notes. 5: 701-704.

TAGster – Single or Multi-Population Tag SNPs Selection, Evaluation and Visualization

TAGster

:: DESCRIPTION

TAGster is a tool to select, evaluate and visualize LD tag SNPs for single or multiple populations

::DEVELOPER

Jack A. Taylor, M.D., Ph.D. , Zongli Xu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX

:: DOWNLOAD

 TAGster

:: MORE INFORMATION

Citation:

Xu Z, Kaplan NL, Taylor JA.
TAGster: efficient selection of LD tag SNPs in single or multiple populations.
Bioinformatics. 2007 23:3254-5. Epub 2007 Sep 7