AntigenMap 1.0 / AntigenMap 3D – 3D / Antigenic Cartography Construction

AntigenMap 1.0 / AntigenMap 3D

:: DESCRIPTION

AntigenMap is a webserver run and/or standalone program for antigenic cartography construction

AntigenMap 3D is a web application for generating 3D antigenic maps

::DEVELOPER

Systems Biology Laboratory, College of Veterinary Medicine,Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows / MacOsX
  • Java

:: DOWNLOAD

  AntigenMap

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2010 Oct 7;6(10):e1000949. doi: 10.1371/journal.pcbi.1000949.
A computational framework for influenza antigenic cartography.
Cai Z, Zhang T, Wan XF.

Bioinformatics. 2012 May 1;28(9):1292-3. doi: 10.1093/bioinformatics/bts105.
AntigenMap 3D: an online antigenic cartography resource.
Barnett JL, Yang J, Cai Z, Zhang T, Wan XF.

EDTSurf – Quick and Accurate Construction of Macromolecular Surfaces

EDTSurf

:: DESCRIPTION

EDTSurf is a open source program to construct triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface). EDTsurf also identifies cavities which are inside of macromolecules.

:DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
:: DOWNLOAD

  EDTSurf

:: MORE INFORMATION

Citation

D. Xu, Y. Zhang (2009)
Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform.
PLoS ONE 4(12): e8140.

ERA v1 – Efficient Serial and Parallel Suffix Tree Construction

ERA v1

:: DESCRIPTION

ERA (Elastic Range), a disk-based suffix tree construction method, which works efficiently with very long strings that are much larger than the available memory.

::DEVELOPER

InfoCloud Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C Compiler

:: DOWNLOAD

 ERA

:: MORE INFORMATION

Citation:

Essam Mansour, Amin Allam, Spiros Skiadopoulos, Panos Kalnis:
ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings.
PVLDB 5(1): 49-60 (2011)

Mercator 2013.01.11 – Multiple Whole-Genome Orthology Map Construction

Mercator 2013.01.11

:: DESCRIPTION

MERCATOR is an orthology mapping program suitable for multiple genomes.Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term “syntenic” is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an ancestral genome. However, it has been pointed out that this use of the term is incorrect (Passarge et al. 1999) and thus we will use the terms “homologous”, “orthologous”, and “paralogous” instead. Ideally, given K genomes, we would like to identify all orthologous genomic regions as well as paralogous regions within each genome and hypothetical ancestral genome. Maps listing these relationships are extremely valuable to researchers performing comparative analyses of genomic sequence.

::DEVELOPER

Colin DeweyPachter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Mercator

:: MORE INFORMATION

Citation

Colin N. Dewey, Peter M. Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter
Parametric Alignment of Drosophila Genomes
PLoS Comput Biol 2(6): e73. doi:10.1371/journal.pcbi.0020073

Faucet v0.5 – Streaming de novo Assembly Graph Construction

Faucet v0.5

:: DESCRIPTION

Faucet is an streaming metagenome assembler. It uses low memory and disk space and achieves highly contiguous assemblies.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Faucet

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Jan 1;34(1):147-154. doi: 10.1093/bioinformatics/btx471.
Faucet: streaming de novo assembly graph construction.
Rozov R, Goldshlager G, Halperin E, Shamir R.

DendroUPGMA 201410 – A Dendrogram Construction Utility

DendroUPGMA 201410

:: DESCRIPTION

Use DendroUPGMA to create a dendrogram from (a) a set of variables, (b) a similarity matrix or (c) a distance matrix. The program calculates a similarity matrix (only for option a), transforms similarity coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm.

::DEVELOPER

P. Puigbo, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

S. Garcia-Vallve, J. Palau and A. Romeu (1999)
Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis.
Molecular Biology and Evolution 9:1125-1134.

SaffronTree v0.1.2 – Reference Free Rapid Phylogenetic Tree Construction from raw read data

SaffronTree v0.1.2

:: DESCRIPTION

SaffronTree takes FASTQ/FASTA files as input and uses a kmer analysis to build a phylogenetic neighbour joining tree in newick format.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SaffronTree

:: MORE INFORMATION

Gen3D – 3D Genome and Chromosome Structural Model Construction

Gen3D

:: DESCRIPTION

Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations.

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 Gen3D

:: MORE INFORMATION

Citation

Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data.
Nowotny J, Ahmed S, Xu L, Oluwadare O, Chen H, Hensley N, Trieu T, Cao R, Cheng J.
BMC Bioinformatics. 2015 Oct 23;16(1):338.

XiP 3.0 – Construction of Workflows

XiP 3.0

:: DESCRIPTION

XiP (eXtensible integrative Pipeline) is a flexible, editable and modular environment with a user-friendly interface that does not require previous programming skills to run,construct and edit workflows. XiP allows the construction of workflows by linking components written in both R and Java, the analysis of high-throughput data in grid engine systems and also the development of customized pipelines that can be encapsulated in a package and distributed.

::DEVELOPER

Nagasaki Lab

:: SCREENSHOTS

XiP

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 XiP

:: MORE INFORMATION

Citation

Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, Li C, Miyano S.
XiP: a computational environment to create, extend and share workflows.
Bioinformatics. 2013 Jan 1;29(1):137-9

Vernan – Specification, Construction, and Exact Reduction of State Transition System models of Biochemical Processes

Vernan

:: DESCRIPTION

Vernan is a MATLAB tool for the specification, construction, and exact reduction of state transition system models of biochemical processes

::DEVELOPER

The Virtual Physiological Rat Project

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • MatLab

:: DOWNLOAD

 Vernan

:: MORE INFORMATION

Citation

Bugenhagen SM, Beard DA.
Specification, construction, and exact reduction of state transition system models of biochemical processes.
J. Chem. Phys. 137, 2012