:: DESCRIPTION
AliView is an alignment viewer and editor designed to meet the requirements of next generation sequencing era phylogenetic datasets.
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:: MORE INFORMATION
Citation
Bioinformatics. 2014 Aug 5. pii: btu531.
AliView: a fast and lightweight alignment viewer and editor for large data sets.
Larsson A.
:: DESCRIPTION
ApE (A Plasmid Editor) is an integrated program for plasmid construction and visualization. It includes a sequence editor, a linear text map identifying sequence features such as restriction sites and ORFs, and a graphic view that highlights sites and features in your sequences. A program designed by a molecular biologist, for molecular biologists.
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:: DOWNLOAD
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:: DESCRIPTION
Tundra is a piechart visualization and edition software for displaying bioinformatic data.
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Millenium Institute of Oceanography
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:: DESCRIPTION
Baobab is an editor for large phylogenetic trees written in Java. It allows you to create and/or modify a tree interactively, adding/(re)moving branches and nodes, changing leave names, setting parameters. Baobab focuses on edition, not representation and display that are only used as a tool to make edition easier.
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Citation:
Dutheil J, Galtier N.
BAOBAB: a Java editor for large phylogenetic trees.
Bioinformatics. 2002 Jun;18(6):892-3.
:: DESCRIPTION
Jalview is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.
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:: MORE INFORMATION
Citation:
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
“Jalview Version 2 – a multiple sequence alignment editor and analysis workbench”
Bioinformatics 25 (9) 1189-1191
:: DESCRIPTION
iMotifs is a graphical motif analysis environment for the Apple Mac computers (Leopard or later).It allows visualization of annotated sequence motifs and scored motif hits in sequences.
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Citation
Bioinformatics. 2010 Mar 15;26(6):843-4. doi: 10.1093/bioinformatics/btq026. Epub 2010 Jan 26.
iMotifs: an integrated sequence motif visualization and analysis environment.
Piipari M1, Down TA, Saini H, Enright A, Hubbard TJ.
:: DESCRIPTION
GenomeView is a next-generation stand-alone genome browser and editor.It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported and new functionality can be added using a plugin system.
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:: MORE INFORMATION
Citation
GenomeView: a next-generation genome browser
Thomas Abeel; Thomas Van Parys; Yvan Saeys; James Galagan; Yves Van de Peer
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr995
:: DESCRIPTION
Dunnart is a prototype constraint-based diagram editor. It includes standard diagram editing capabilities, as well as advanced features such as constraint-based geometric placement tools (alignment, distribution, separation, non-overlap, and page containment), automatic object-avoiding poly-line connector routing, and continuous network layout.
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IALab: Immersive Analytics Lab
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:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Tim Dwyer, Kim Marriott, and Michael Wybrow.
Dunnart: A constraint-based network diagram authoring tool.
In Proceedings of 16th International Symposium on Graph Drawing (GD’08), LNCS 5417, pages 420–431. Springer-Verlag, 2009
:: DESCRIPTION
PhyDE (Phylogenetic Data Editor) is a system-independent editor for DNA and amino acid sequence alignments, designed to assist anybody interested in phylogenetic or other comparative analyses of sequence data.
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:: DESCRIPTION
TreeGraph is a graphical editor for phylogenetic trees which allows you to apply lots of graphical formats to the elements of your tree. Moreover, it supports several (visible or invisible) annotations (e.g. support values) for every branch or node. These annotations can be imported from Nexus tree files or text files containing data in a table (e.g. exported from a spreadsheet program).
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:: MORE INFORMATION
Citation
Stöver B C, Müller K F
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
BMC Bioinformatics 2010, 11:7
