Unrooted – Draw Binary Tree Expressed in the standard Phylogenetic Tree Format

Unrooted

:: DESCRIPTION

Unrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). Trees are drawn in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches.

::DEVELOPER

Unrooted team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows

:: DOWNLOAD

 Unrooted

:: MORE INFORMATION

Fizzy v1.4 – Feature Selection for Biological Data Formats

Fizzy v1.4

:: DESCRIPTION

Fizzy is a feature subset selection tool that uses FEAST in the background to run feature selection on biological data formats.

::DEVELOPER

Drexel’s EESI Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • Python

:: DOWNLOAD

 Fizzy

:: MORE INFORMATION

Citation

Fizzy: feature subset selection for metagenomics.
Ditzler G, Morrison JC, Lan Y, Rosen GL.
BMC Bioinformatics. 2015 Nov 4;16:358. doi: 10.1186/s12859-015-0793-8.

cb2bib 1.5.0 – Manage Bibliographic data in BibTeX Format

cb2bib 1.5.0

:: DESCRIPTION

The cb2Bib is a free, open source, and multiplatform application for rapidly extracting unformatted, or unstandardized bibliographic references from email alerts, journal Web pages, and PDF files.

::DEVELOPER

Pere Constans

:: SCREENSHOTS

cb2bib

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

  cb2bib

:: MORE INFORMATION

CellH5 / CellH5Browser 1.1 – Format for Data Exchange in High-content screening / Image Browser

CellH5 / CellH5Browser 1.1

:: DESCRIPTION

CellH5 is an HDF5 data format for cell-based assays in high-throughput microscopy, which stores high-dimensional image data along with inter-object relations in graphs

CellH5Browser is an interactive gallery image browser based on the CellH5 data format. For testing download a CellH5 example data set for the CellH5Browser from a time-lapse microscopy dataset.

::DEVELOPER

CellH5 team

:: SCREENSHOTS

CellH5Browser

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R pacakge/ MatLab / Python

:: DOWNLOAD

  CellH5 / CellH5Browser

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jun 15;29(12):1580-2. doi: 10.1093/bioinformatics/btt175. Epub 2013 Apr 16.
CellH5: a format for data exchange in high-content screening.
Sommer C1, Held M, Fischer B, Huber W, Gerlich DW.

iConvert – Convert Genotype Allele Formats

iConvert

:: DESCRIPTION

The iConvert program allows to convert genotype allele formats (any format for any SNP chip contained in the SNPchiMp tool).

::DEVELOPER

iConvert team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • Python

:: DOWNLOAD

 iConvert

:: MORE INFORMATION

Citation

SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species.
Nicolazzi EL, Caprera A, Nazzicari N, Cozzi P, Strozzi F, Lawley C, Pirani A, Soans C, Brew F, Jorjani H, Evans G, Simpson B, Tosser-Klopp G, Brauning R, Williams JL, Stella A.
BMC Genomics. 2015 Apr 10;16(1):283.

SVGenes 0.4.1 -SVG Format Genome Browser Style Pictures

SVGenes 0.4.1

:: DESCRIPTION

SVGenes (bio-svgenes) is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface.

::DEVELOPER

Dan MacLean

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Ruby
  • BioRuby

:: DOWNLOAD

 SVGenes

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1890-2. doi: 10.1093/bioinformatics/btt294. Epub 2013 Jun 6.
SVGenes: a library for rendering genomic features in scalable vector graphic format.
Etherington GJ1, MacLean D.

BIOM-FORMAT 2.1.3 – The Biological Observation Matrix format

BIOM-FORMAT 2.1.3

:: DESCRIPTION

The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome.

::DEVELOPER

BIOM-FORMAT Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BIOM-FORMAT

:: MORE INFORMATION

Citation

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.
Daniel McDonald, Jose C. Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, and J. Gregory Caporaso.
GigaScience 2012, 1:7 doi:10.1186/2047-217X-1-7

Bio-Formats 5.0.8 – Java Library for Reading & Writing Biology Image File Formats

Bio-Formats 5.0.8

:: DESCRIPTION

Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. See the table below for a complete list (click the headers to sort, and format names to see all information).

Bio-Formats’s primary purpose is to convert proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format.

::DEVELOPER

development teams at LOCI at the University of Wisconsin-MadisonUniversity of Dundee and Glencoe Software

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • java

:: DOWNLOAD

Bio-Formats

:: MORE INFORMATION

KEGGtranslator 2.4.0 – Visualizing and Converting the KEGG PATHWAY database to various formats

KEGGtranslator 2.4.0

:: DESCRIPTION

KEGGtranslator is an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g., MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator converts KEGG files (KGML formatted XML-files) to SBML, BioPAX, SIF, SBGN, SBML-qual, GML, GraphML, JPG, GIF, LaTeX, etc.

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

KEGGtranslator

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

   KEGGtranslator

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 15;27(16):2314-5. doi: 10.1093/bioinformatics/btr377. Epub 2011 Jun 23.
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.
Wrzodek C, Dräger A, Zell A.