iTOL 5.2 – Display & Manipulation of Phylogenetic Trees

iTOL 5.2

:: DESCRIPTION

iTOL (Interactive Tree Of Life) is an online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize mid-sized trees (up to several thousand leaves). Trees can be exported to several graphical formats, both bitmap and vector based.

::DEVELOPER

Bork Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser (Firefox)

:: DOWNLOAD

 iTOL

:: MORE INFORMATION

Citation

Interactive Tree Of Life (iTOL) v4: recent updates and new developments.
Letunic I, Bork P.
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259. doi: 10.1093/nar/gkz239.

Bioinformatics. 2007 Jan 1;23(1):127-8. Epub 2006 Oct 18.
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
Letunic I, Bork P.

Letunic I and Bork P (2011)
Nucleic Acids Res doi: 10.1093/nar/gkr201
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

GeneDesign 5.54 – Codon Manipulation for ORFs

GeneDesign 5.54

:: DESCRIPTION

GeneDesign is a codon manipulation library. Its main purpose is to ease the design and assembly of synthetic DNA.

::DEVELOPER

Joel Bader lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 GeneDesign

:: MORE INFORMATION

Citation

Design-A-Gene with GeneDesign.
Richardson SM, Liu S, Boeke JD, Bader JS.
Methods Mol Biol. 2012;852:235-47. doi: 10.1007/978-1-61779-564-0_18.

RedeR 1.18.0 – Interactive Visualization and Manipulation of Nested Networks

RedeR 1.18.0

:: DESCRIPTION

RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of modular structures, nested networks and multiple levels of hierarchical associations.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 RedeR

:: MORE INFORMATION

Citation

Genome Biol. 2012 Apr 24;13(4):R29. doi: 10.1186/gb-2012-13-4-r29.
RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.
Castro MA1, Wang X, Fletcher MN, Meyer KB, Markowetz F.

Brain 1.5.1 – Library for Biomedical Knowledge Manipulation

Brain 1.5.1

:: DESCRIPTION

Brain helps you to quickly and easily buid OWL ontologies and knowledge bases.

::DEVELOPER

Samuel Croset

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 Brain

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 1;29(9):1238-9. doi: 10.1093/bioinformatics/btt109. Epub 2013 Mar 16.
Brain: biomedical knowledge manipulation.
Croset S1, Overington JP, Rebholz-Schuhmann D.

PlasmaDNA 1.4.2 – PLAsmid MAnipulation program

PlasmaDNA 1.4.2

:: DESCRIPTION

PlasmaDNA is a new, free DNA analysis and manipulation software. It is simple to learn and to use, and contains multiple features designed to help with:

The design of a successful cloning strategy
The generation of the sequences of new clones
The archiving of the cloning strategy

::DEVELOPER

Alexandre Angers-Loustau, Ph.D.
+358 9 191 25142
Haartmaninkatu 8
alexandre.angers-loustau (at) helsinki.fi

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

PlasmaDNA

:: MORE INFORMATION

Citation:

Alexandre Angers-Loustau , Jeffrey Rainy and Kirmo Wartiovaara
PlasmaDNA: a free, cross-platform plasmid manipulation program for molecular biology laboratories
BMC Molecular Biology 2007, 8:77

RnamlView 1.0 – Manipulation, Storage & Visualisation of RNA Data

RnamlView 1.0

:: DESCRIPTION

RnamlView is a visualization tool that displays/edits 2-dimensional diagrams of RNA/DNA secondary structures with tertiary interactions created by RNAView (above). The application generates standard molecular representations (e.g. tRNA cloverleaf structures) or any structural representation desired by the user by rearranging various parts (e.g helices and single strands) of the RNAView 2D diagrams. RNA motifs are rapidly identified and classified with the base pair annotation and the 2D graphic display.

::DEVELOPER

Fabrice Jossinet, & Eric Westhof, Institut de biologie moleculaire et cellulaire du CNRS

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

RnamlView

:: MORE INFORMATION

Citation

Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H.M., Westhof, E. (2003).
Tools for the automatic identification and classification of RNA base pairs.
Nucleic Acids Research 31.13: 3450-3460.

GP 0.26 / Arka 0.11 – Sequence Manipulation tools

GP 0.26 / Arka 0.11

:: DESCRIPTION

GP and Arka are very leightweighed programs for manipulation of DNA / RNA / protein sequences. They are designed on one hand to run smoothly on older machines, and on the other — to faciliate processing of large numbers of sequence / data files. GP includes utilities to convert DNA / RNA to protein, determine codon usage / GC contents, promotor searches, Tm, searching for restriction sites, converting sequences into numerical representations and much more.

::DEVELOPER

Dr. January Weiner 3rd

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GP  / Arka

:: MORE INFORMATION

Mol2Mol 5.6.3 – Molecule File Manipulation & Conversion

Mol2Mol 5.6.3

:: DESCRIPTION

Mol2Mol is a menu-driven program that converts between the file formats used by the major PC modeling programs.

Mol2Mol recognizes, reads and writes about 50 different file formats and subformats. It contains a simple graphic display module to inspect the currently loaded molecule. It possesses some chemical intelligence for recognizing detailed atom types, hybridization and chemical environments, which is necessary for converting simpler formats (like X-ray crystallographic files) to more advanced ones, or when hydrogen atoms are automatically to be added to the heavy atoms. Problematic files can be corrected within Mol2mol or as ASCII files by calling directly your favourite text editor.

Mol2Mol can convert molecular files into POV-Ray files. As with POV-Ray in general, you can create not only serious scientific illustrations, but surrealistic or funny images as well.

::DEVELOPER

Dr. Tamas E. Gunda

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Mol2Mol trial version

:: MORE INFORMATION

Mol2Mol is a shareware. Mol2Mol single user licence: € 39.  Buy Mol2Mol now via Share-It! with your credit card.

SMS 2 – Sequence Manipulation Suite

SMS 2

:: DESCRIPTION

SMS (Sequence Manipulation Suite) is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.

::DEVELOPER

Stothard Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Internet Browser
  • java

:: DOWNLOAD

SMS

:: MORE INFORMATION

Citation

Stothard P (2000)
The Sequence Manipulation Suite: JavaScript programs for analyzing and formatting protein and DNA sequences.
Biotechniques 28:1102-1104.