Homed 6.8 – HOMologous sequence EDitor

Homed 6.8

:: DESCRIPTION

Homed is a MacOs X application for displaying and editing multiple sequence alignments.

::DEVELOPER

Department of Biochemistry, University of Otago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 Homed

:: MORE INFORMATION

Citation

HOMED: a homologous sequence editor.
Stockwell PA.
Trends Biochem Sci. 1988 Aug;13(8):322-4. PMID: 3154284

SSEdit 6.08 – Single (Short) Sequence Editor

SSEdit 6.08

:: DESCRIPTION

SSEdit is a MacOS X application for viewing and editing single sequences.  Input and output files in FASTA, NRBF, Staden and other formats are supported with the capability to recognise some by the file extension name.

::DEVELOPER

Department of Biochemistry, University of Otago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 SSEdit

:: MORE INFORMATION

Avogadro2 1.90 – Molecule Editor & Visualizer

Avogadro2 1.90

:: DESCRIPTION

Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

::DEVELOPER

Avogadro team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

Avogadro

:: MORE INFORMATION

Citation

J Cheminform. 2012 Aug 13;4(1):17. doi: 10.1186/1758-2946-4-17.
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.
Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR.

AliView 1.27 – Alignment Viewer and Editor for large data sets

AliView 1.27

:: DESCRIPTION

AliView is an alignment viewer and editor designed to meet the requirements of next generation sequencing era phylogenetic datasets.

::DEVELOPER

Anders Larsson

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /Windows/ MacOsX

:: DOWNLOAD

 AliView

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Aug 5. pii: btu531.
AliView: a fast and lightweight alignment viewer and editor for large data sets.
Larsson A.

ApE 3.0.3 – A Plasmid Editor

ApE 3.0.3

:: 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.

::DEVELOPER

M. Wayne Davis

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX / Windows / Linux
  • Tcl/Tk

:: DOWNLOAD

ApE

:: MORE INFORMATION

Apollo 2.6.4 – Genome Annotation Viewer & Editor

Apollo 2.6.4

:: DESCRIPTION

Apollo is the first instantaneous, collaborative genomic annotation editor available on the Web.

Web Apollo is designed to support geographically dispersed researchers, and the work of a distributed community is coordinated through automatic synchronization: all edits in one client are instantly pushed to all other clients, allowing users to see annotation updates from collaborators in real-time during the editing process.

::DEVELOPER

Apollo team

:: SCREENSHOTS

:: REQUIREMENTS

  • Mac OsX / Linux /Solaris / Unix
  • Tomcat
  • Perl
  • BioPerl
  • Blat
  • JAVA

:: DOWNLOAD

Apollo

:: MORE INFORMATION

Citation:

Dunn NA, Unni DR, Diesh C, Munoz-Torres M, Harris NL, Yao E, Rasche H, Holmes IH, Elsik CG, Lewis SE.
Apollo: Democratizing genome annotation.
PLoS Comput Biol. 2019 Feb 6;15(2):e1006790. doi: 10.1371/journal.pcbi.1006790. PMID: 30726205; PMCID: PMC6380598.

Baobab 3.31 – Editor for Large Phylogenetic Trees

Baobab 3.31

:: 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.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

Baobab

:: MORE INFORMATION

Citation:

Dutheil J, Galtier N.
BAOBAB: a Java editor for large phylogenetic trees.
Bioinformatics. 2002 Jun;18(6):892-3.

Jalview 2.11.1.4 – Multiple Alignment Editor

Jalview 2.11.1.4

:: 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.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

Jalview

:: 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

iMotifs 0.2.5 – Sequence Motif Editor for the Mac

iMotifs 0.2.5

:: 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.

::DEVELOPER

iMotifs team

:: SCREENSHOTS

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

 iMotifs

:: MORE INFORMATION

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.