RnaViz 2.0.3 – Secondary Structure Drawings of RNA Molecules

RnaViz 2.0.3

:: DESCRIPTION

RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure can be changed easily. Display of special structural elements such as pseudo-knots or unformatted areas is possible. Sequences can be automatically numbered, and several other types of labels can be used to annotate particular bases or areas. Although the program does not try to produce an initially non-overlapping drawing, the layout of a properly positioned structure drawing can be applied to newly created drawing using skeleton files. In this way a range of similar structures can be drawn with a minimum of effort. Skeletons for several types of RNA molecule are included with the program.

::DEVELOPER

Peter De Rijk

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

RnaViz

:: MORE INFORMATION

Citation

Peter De Rijk, Jan Wuyts and Rupert De Wachter (2003)
RnaViz2: an improved representation of RNA secondary structure.
Bioinformatics 19(2): 299-300

VARUS 1.0.0 – Drawing Diverse Samples from RNA-Seq Libraries

VARUS 1.0.0

:: DESCRIPTION

VARUS automates the selection and download of a limited number of RNA-seq reads from at NCBI’s Sequence Read Archive (SRA) targeting a sufficiently high coverage for many genes for the purpose of gene-finder training and genome annotation.

::DEVELOPER

Bioinformatics Greifswald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

VARUS

:: MORE INFORMATION

Citation

Stanke M, Bruhn W, Becker F, Hoff KJ.
VARUS: sampling complementary RNA reads from the sequence read archive.
BMC Bioinformatics. 2019 Nov 8;20(1):558. doi: 10.1186/s12859-019-3182-x. PMID: 31703556; PMCID: PMC6842140.

PathWhiz 1.0 – Pathway Drawing Web Server

PathWhiz 1.0

:: DESCRIPTION

PathWhiz is a web server designed for the creation of colourful, visually pleasing, and biologically accurate pathway diagrams that are machine-readable and interactive.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Pathways with PathWhiz.
Pon A, Jewison T, Su Y, Liang Y, Knox C, Maciejewski A, Wilson M, Wishart DS.
Nucleic Acids Res. 2015 May 1. pii: gkv399

TreeView X 0.5-1 – Tree Drawing Software

TreeView X 0.5-1

:: DESCRIPTION

TreeView X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP, ClustalX, TREE-PUZZLE, and other programs). It has a subset of the functionality of the version of TreeView available for the Mac Classic and Windows

::DEVELOPER

Professor Rod Page

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

 TreeView X

:: MORE INFORMATION

Citation

Page, R. D. M. 1996.
TREEVIEW: An application to display phylogenetic trees on personal computers.
Computer Applications in the Biosciences 12: 357-358.

NJplot 2.4 – Phylogenetic Tree Drawing Program

NJplot 2.4

:: DESCRIPTION

NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

NJplot

:: MORE INFORMATION

Citation

Perrière, G. and Gouy, M. (1996)
WWW-Query: An on-line retrieval system for biological sequence banks.
Biochimie, 78, 364-369.

Peditree 2005 – Plant Pedigree Tree Drawing & Analysis

Peditree 2005

:: DESCRIPTION

PediTree is a software package to recursively analyse plant pedigree data which is arranged in a simple-single table database structure.

Peditree will lookup the parents of a variety/cultivar, then the parents of the parents (grandparents)and so on. The result is displayed in a explorer style, collapsible tree or a pedigree drawing (see images below; click to enlarge).

::DEVELOPER

Wageningen UR Plant Breeding

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Peditree

:: MORE INFORMATION

Citation

J Hered. 2005 Jul-Aug;96(4):465-8. Epub 2005 Apr 13.
Peditree: pedigree database analysis and visualization for breeding and science.
van Berloo R, Hutten RC.

XDrawChem 1.9.9 – Molecule Structure Drawing

XDrawChem 1.9.9

:: DESCRIPTION

XDrawChem is a two-dimensional molecule drawing program. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS.

::DEVELOPER

Bryan Herger , bherger@users.sourceforge.net

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

XDrawChem

:: MORE INFORMATION

PedigreeQuery 20080410 – Drawing Pedigrees step-by-step

PedigreeQuery 20080410

:: DESCRIPTION

PedigreeQuery is a program for working with large pedigrees. Some times it is required to get chart only of some shapes of such pedigrees. PedigreeQuery was made for drawing shapes of pedigrees using step-by-step algorithm. The drawing unit is a nuclear family. New nuclear family is added to pictured shape of pedigree on each step. Enlargement of shape is making by pointing on person who is already in shape and we will called him pointer. If there are offspring or parents of the pointer which are not yet in the shape they will added to it. Step-by-step algorithm allows to draw any shape of pedigrees or whole pedigrees.

::DEVELOPER

Laboratory of the Methods of Genetic Analysis , Institute of Cytology and Genetics, Novosibirsk, Russia.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux
  • Java

:: DOWNLOAD

 PedigreeQuery

:: MORE INFORMATION

Citation:

Genetika. 2004 Oct;40(10):1425-8.
[An algorithm of step-by-step pedigree drawing].
[Article in Russian]
Kirichenko AV.

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