Jalview 2.11.0 – Multiple Alignment Editor

Jalview 2.11.0

:: 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

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.

PhyDE2 0.2.0 – Phylogenetic Data Editor

PhyDE2 0.2.0

:: 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.

::DEVELOPER

BioInfWeb projects

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

PhyDE

:: MORE INFORMATION

TreeGraph 2.15.0 – Graphical Editor for Phylogenetic Trees

TreeGraph 2.15.0

:: 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).

::DEVELOPER

BioInfWeb projects,

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

TreeGraph

:: MORE INFORMATION

Citation

Stöver B C, Müller K F
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
BMC Bioinformatics 2010, 11:7

BioEdit 7.2.5 – Biological Sequence Alignment Editor

BioEdit 7.2.5

:: DESCRIPTION

BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP.  An intuitive multiple document interface with convenient features  makes alignment and manipulation  of sequences relatively easy on your desktop computer.    Several sequence manipulation and analysis options and links to external anaylsis programs facilitate a working environment which allows you to view and manipulate sequences with simple point-and-click operations.

::DEVELOPER

Tom Hall

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

BioEdit

:: MORE INFORMATION

Chromas 2.6.6 / ChromasPro 2.1.8 – Sequence & Chromatogram Editor

Chromas 2.6.6 / ChromasPro 2.1.8

:: DESCRIPTION

Chromas is a low-cost chromatogram file editor with search, vector sequence detection and multi-format sequence export functions, plus powerful batch processing.

ChromasPro is a low-cost sequence and chromatogram editor with search, vector sequence detection, contiguous sequence assembly and restriction and open-reading-frame mapping.

::DEVELOPER

Technelysium Pty Ltd

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Chromas ,  ChromasPro

:: MORE INFORMATION

Web Apollo 2.0.2 – Genome Annotation Viewer & Editor

Web Apollo 2.0.2

:: DESCRIPTION

Web 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

Web Apollo team

:: SCREENSHOTS

WebApollo

:: REQUIREMENTS

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

:: DOWNLOAD

Web Apollo

:: MORE INFORMATION

Web Apollo is governed by Copyright to the Regents of the University of California. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the conditions stated in this license are met. To learn more, please visit https://github.com/GMOD/Apollo/blob/master/LICENSE.md

Citation:

Apollo: a sequence annotation editor. Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Ricter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews B, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME (2002). Genome Biology 2002, 3(12):research0082

Web Apollo: a web-based genomic annotation editing platform.
Lee E, Helt GA, Reese JT, Munoz-Torres MC, Childers CP, Buels RM, Stein L, Holmes IH, Elsik CG, Lewis SE.
Genome Biol. 2013 Aug 30;14(8):R93.

ApE 2.0.49 – A Plasmid Editor

ApE 2.0.49

:: 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