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      Jalview Version 2—a multiple sequence alignment editor and analysis workbench

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Summary: Jalview Version 2 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 2 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.

          Availability: The Jalview 2 Desktop application and JalviewLite applet are made freely available under the GPL, and can be downloaded from www.jalview.org

          Contact: g.j.barton@dundee.ac.uk

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          SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny.

          Mathieu N. Galtier, C Gautier, M Gouy (1996)
          SEAVIEW and PHYLO_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEAVIEW is a sequence alignment editor allowing manual or automatic alignment through an interface with CLUSTALW program. Alignment of large sequences with extensive length differences is made easier by a dot-plot-based routine. The PHYLO_WIN program allows phylogenetic tree building according to most usual methods (neighbor joining with numerous distance estimates, maximum parsimony, maximum likelihood), and a bootstrap analysis with any of them. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse and stored into sequence files, thus avoiding multiple data files. Both tools are entirely mouse driven. On-line help makes them easy to use. They are freely available by anonymous ftp at biom3.univ-lyon1.fr/pub/ mol_phylogeny or http:@acnuc.univ-lyon1.fr/, or by e-mail to galtier@biomserv.univ-lyon1.fr.
          Article 0 comments Cited 311 times – based on 0 reviews     Review now
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            The Distributed Annotation System

            Robin D Dowell, Rodney Jokerst, Allen Day … (2001)
            Background Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory. Results Here we introduce a concept called the Distributed Annotation System (DAS). DAS allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. The communication between client and servers in DAS is defined by the DAS XML specification. Annotations are displayed in layers, one per server. Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example. Conclusions The DAS specification is being used experimentally by Ensembl, WormBase, and the Berkeley Drosophila Genome Project. Continued success will depend on the readiness of the research community to adopt DAS and provide annotations. All components are freely available from the project website .
            Article 0 comments Cited 142 times – based on 0 reviews     Review now
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              SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny

              N Galtier, C Gautier, M Gouy (1996)
              SEAVIEW and PHYLO_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEAVIEW is a sequence alignment editor allowing manual or automatic alignment through an interface with CLUSTALW program. Alignment of large sequences with extensive length differences is made easier by a dot-plot-based routine. The PHYLO_WIN program allows phylogenetic tree building according to most usual methods (neighbor joining with numerous distance estimates, maximum parsimony, maximum likelihood), and a bootstrap analysis with any of them. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse and stored into sequence files, thus avoiding multiple data files. Both tools are entirely mouse driven. On-line help makes them easy to use. They are freely available by anonymous ftp at biom3.univ-lyon1.fr/pub/ mol_phylogeny or http:@acnuc.univ-lyon1.fr/, or by e-mail to galtier@biomserv.univ-lyon1.fr.
              Article 0 comments Cited 130 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Bioinformatics
                Journal ID (publisher-id): bioinformatics
                Journal ID (hwp): bioinfo
                Title: Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1367-4803
                ISSN (Electronic): 1460-2059
                Publication date (Print): 1 May 2009
                Publication date (Electronic): 16 January 2009
                Publication date PMC-release: 16 January 2009
                Volume: 25
                Issue: 9
                Pages: 1189-1191
                Affiliations
                1School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK and 2Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
                Author notes
                *To whom correspondence should be addressed.

                †The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

                ‡Present address: Genome Exploration Research Group, RIKEN Omics Science Center and the Functional RNA Research Program, Frontier Research System, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa 230-0045, Japan.

                Associate Editor: Jonathan Wren

                Article
                Publisher ID: btp033
                DOI: 10.1093/bioinformatics/btp033
                PMC ID: 2672624
                PubMed ID: 19151095
                SO-VID: 51f7afa0-1e61-4431-a2ac-b282882688e9
                Copyright © © 2009 The Author(s)
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 24 November 2008
                Date revision received : 24 November 2008
                Date accepted : 8 January 2009
                Categories
                Subject: Applications Note
                Subject: Sequence Analysis

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology

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