CopyCat 2.04 – Co-phylogenetic Analysis Tool

CopyCat 2.04

:: DESCRIPTION

CopyCat provides an easy and fast access to cophylogenetic analyses. It incorporates a wrapper for the program ParaFit, which conducts a statistical test for the presence of congruence between host and parasite phylogenies.

::DEVELOPER

Jan P. Meier-KolthoffAlexander F. AuchDaniel H. Huson, and Markus Göker.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

CopyCat

:: MORE INFORMATION

Citation:

Jan P. Meier-Kolthoff, Alexander F. Auch, Daniel H. Huson, Markus G?ker.
COPYCAT: Co-phylogenetic Analysis tool.
Bioinformatics, 23(7):898-900, 2007.

Staden 2.0.0b11 – DNA Sequence Assembly , Editing and Analysis

Staden 2.0.0b11

:: DESCRIPTION

Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) .

::DEVELOPER

Staden Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Staden

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jul 15;26(14):1699-703. doi: 10.1093/bioinformatics/btq268. Epub 2010 May 30.
Gap5–editing the billion fragment sequence assembly.
Bonfield JK1, Whitwham A.

Rodger Staden, David P. Judge and James K. Bonfield.
Analysing Sequences Using the Staden Package and EMBOSS.
Introduction to Bioinformatics. A Theoretical and Practical Approach. Eds. Stephen A. Krawetz and David D. Womble. Human Press Inc., Totawa, NJ 07512 (2003)

JABAWS 2.2 – JAva Bioinformatics Analysis Web Services

JABAWS 2.2

:: DESCRIPTION

JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs from Jalview. JABAWS is free software which provides web services conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. Services for multiple sequence alignment include Clustal Omega, Clustal W, MAFFT, MUSCLE, TCOFFEE and PROBCONS. Analysis services allow prediction of protein disorder with DisEMBL, IUPred, Ronn and GlobPlot; and calculation of amino acid alignment conservation with AACon.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX/ Amazon EC2
  • Java

:: DOWNLOAD

 JABAWS

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 15;27(14):2001-2. doi: 10.1093/bioinformatics/btr304. Epub 2011 May 18.
Java bioinformatics analysis web services for multiple sequence alignment–JABAWS:MSA.
Troshin PV, Procter JB, Barton GJ.

VANTED 2.6.5 – Visualization and Analysis of Networks containing Experimental Data

VANTED 2.6.5

:: DESCRIPTION

VANTED (Visualisation and Analysis of Networks containing Experimental Data) is an open source software that offers the possibility to load and edit graphs, which may represent biological pathways or functional hierarchies. It allows to integrate different *omics data into the functional context and provides a variety of functions for data mapping and processing, statistical analysis, and visualisation. With the VANTED Add-on interface it is easily possible to extend the functionality of the software.

::DEVELOPER

VANTED Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 VANTED

:: MORE INFORMATION

Citation

Klukas and Schreiber (2010)
Integration of -omics data and networks for biomedical research with VANTED.
Journal of Integrative Biology, 7(2)

Björn H. Junker, Christian Klukas and Falk Schreiber (2006)
VANTED: A system for advanced data analysis and visualization in the context of biological networks.
BMC Bioinformatics, 7:109

ReadXplorer 2.2.3 – Visualization and Analysis of Mapped Sequences

ReadXplorer 2.2.3

:: DESCRIPTION

ReadXplorer is a freely available comprehensive exploration and evaluation tool for NGS data. It extracts and adds quantity and quality measures to each alignment in order to classify the mapped reads. This classification is then taken into account for the different data views and all supported automatic analysis functions.

::DEVELOPER

Bioinformatics and Systems Biology, Justus-Liebig-University

:: SCREENSHOTS

ReadXplorer

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 ReadXplorer

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 30. [Epub ahead of print]
ReadXplorer – Visualization and Analysis of Mapped Sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A.

MEGAN 6.4.8 – Metagenome analysis

MEGAN 6.4.8

:: DESCRIPTION

MEGAN (MEta Genome ANalyzer) allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets.

::DEVELOPER

Daniel Huson’s Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

 MEGAN

:: MORE INFORMATION

Citation

Analysis of 16S rRNA environmental sequences using MEGAN.
Mitra S, Stärk M, Huson DH.
BMC Genomics. 2011 Nov 30;12 Suppl 3:S17. doi: 10.1186/1471-2164-12-S3-S17.

SeqMonk 0.34.0 – Visualisation and Analysis of Mapped Sequence Data

SeqMonk 0.34.0

:: DESCRIPTION

SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • Java 

:: DOWNLOAD

 SeqMonk

:: MORE INFORMATION

GLAD 2.36.0 – Gain and Loss Analysis of DNA

GLAD 2.36.0

:: DESCRIPTION

The GLAD algorithms aims at identifying the chromosomal regions with identical DNA copy number, which are delimited by breakpoints.

::DEVELOPER

U900 Institut Curie – INSERM/Mines ParisTech “Bioinformatics and Computational Systems Biology of Cancer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

 GLAD

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Dec 12;20(18):3413-22. Epub 2004 Sep 20.
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions.
Hupé P, Stransky N, Thiery JP, Radvanyi F, Barillot E.

Imaris 8.3 – Analysis, Segmentation and Interpretation of 3D and 4D Microscopy datasets

Imaris 8.3

:: DESCRIPTION

Imaris is Bitplane’s core scientific software module for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets.

::DEVELOPER

BITPLANE AG

:: SCREENSHOTS

Imaris

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

 Imaris

:: MORE INFORMATION

bcbio-nextgen 0.9.7 – Best-practice pipelines for fully automated High Throughput Sequencing analysis

bcbio-nextgen 0.9.7

:: DESCRIPTION

bcbio-nextgen is a python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.

::DEVELOPER

Blue Collar Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 bcbio-nextgen

:: MORE INFORMATION