Seqotron v1.0.1 – Alignment Editor for Mac OS X

Seqotron v1.0.1

:: DESCRIPTION

Seqotron is a user-friendly sequence editor. It is written in Objective-C/Cocoa and runs on Mac OS X.

::DEVELOPER

Mathieu Fourment

 SCREENSHOTS

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

Seqotron

:: MORE INFORMATION

CitationFourment M, Holmes EC.
Seqotron: a user-friendly sequence editor for Mac OS X.
BMC Res Notes. 2016 Feb 17;9:106. doi: 10.1186/s13104-016-1927-4. PMID: 26887850; PMCID: PMC4756450.

 

Apollo 2.6.5 – Genome Annotation Viewer & Editor

Apollo 2.6.5

:: 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

WebApollo

:: 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.

OBO-Edit 2.3.1 – Ontology Editor for Biologists

OBO-Edit 2.3.1

:: DESCRIPTION

OBO-Edit is an open source, platform-independent application for viewing and editing any OBO format ontologies. OBO-Edit is a graph-based tool; its emphasis on the overall graph structure of an ontology provides a friendly interface for biologists, and makes OBO-Edit excellent for the rapid generation of large ontologies focusing on relationships between relatively simple classes.

::DEVELOPER

OBO-Edit Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 OBO-Edit

:: MORE INFORMATION

Citation

OBO-Edit–an ontology editor for biologists.
Day-Richter J, Harris MA, Haendel M; Gene Ontology OBO-Edit Working Group, Lewis S.
Bioinformatics. 2007 Aug 15;23(16):2198-200. Epub 2007 Jun 1.

Edinburgh Pathway Editor 3.0a13 – Visual Editor for Systems Biology

Edinburgh Pathway Editor 3.0a13

:: DESCRIPTION

EPE (Edinburgh Pathway Editor) is a visual editor for Systems Biology. It allows you to draw Graphical Notations commonly used in Systems Biology. In particular it supports Systems Biology Graphical Notations (SBGN).

::DEVELOPER

SynthSys (formerly CSBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Edinburgh Pathway Editor

:: MORE INFORMATION

Citation:

A. Sorokin, K. Paliy, A. Selkov, O. V. Demin, S. Dronov, P. Ghazal, I. Goryanin
The pathway editor: a tool for managing complex biological networks
IBM Journal of Research and Development , Nov. 2006 ,Volume: 50 Issue:6 ,p561 – 573

ChiBE 2.2 – Chisio BioPAX Editor

ChiBE 2.2

:: DESCRIPTION

ChiBE (Chisio BioPAX Editor)is a free editing and visualization tool for pathway models represented by the BioPAX format, based on Chisio.

::DEVELOPER

Bilkent Center for Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 ChiBE

:: MORE INFORMATION

Citation

O. Babur, U. Dogrusoz, E. Demir, and C. Sander,
ChiBE: interactive visualization and manipulation of BioPAX pathway models“,
Bioinformatics, 26(3), pp. 429-431, 2010.

Squint 1.02 – Multiple Sequence Alignment Editor

Squint 1.02

:: DESCRIPTION

Squint is an advanced alignment tool. It brings together algorithmic alignment of molecular sequences, with human editing. It is an extension of the alignment editor available in Pebble.

::DEVELOPER

the New Zealand Bioinformatics Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

 Squint

:: MORE INFORMATION

Citation:

Goode, M. and Rodrigo, A. G., (2007),
SQUINT: A multiple alignment program and editor.,
Bioinformatics 23:1553-1555.

CRISPR-SKIP 1.0.1 – Programmable Gene Splicing with Single Base Editors

CRISPR-SKIP 1.0.1

:: DESCRIPTION

The CRISPR-SKIP webtool identifies which exons can be skipped by editing the flanking G nucleotide of the conserved dinucleotide sequence at the splice acceptor site. The base editors supported in this webtool are BE3, SaKKH-BE3, VRER-BE3, VQR-BE3. The genome assembly and gene annotation used are GRCh38 and GENCODE release 26, respectively. Only primary PAMs are considered.

::DEVELOPER

Jun S. Song’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Gapinske M, Luu A, Winter J, Woods WS, Kostan KA, Shiva N, Song JS, Perez-Pinera P.
CRISPR-SKIP: programmable gene splicing with single base editors.
Genome Biol. 2018 Aug 15;19(1):107. doi: 10.1186/s13059-018-1482-5. PMID: 30107853; PMCID: PMC6092781.

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.