From: amwaterhouse Date: Thu, 2 Jun 2005 12:24:29 +0000 (+0000) Subject: *** empty log message *** X-Git-Tag: Release_2_0~119 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c2e381f1c4bba1394b8c0a6d46ac4ea3a1a1c1f8;p=jalview.git *** empty log message *** --- diff --git a/website/help.gif b/website/help.gif new file mode 100755 index 0000000..f95eb55 Binary files /dev/null and b/website/help.gif differ diff --git a/website/index.html b/website/index.html new file mode 100755 index 0000000..176e076 --- /dev/null +++ b/website/index.html @@ -0,0 +1,114 @@ + + + + +JalView - Java alignment editor + + + + + + + +
+ + + + +
+ + + + + +
Jalview +
+
a + multiple alignment editor
+
+
+ + + + + +

Downloads

+ + Examples + Reference + Source Code
    +
  • Jalview 2
    • +
+

Feedback

+

   

+


+ +

+

Jalview is a multiple alignment editor written in java. + It is used widely in a variety of web pages (e.g. the EBI clustalw server + and the PFAM protein domain database) but is available as a general + purpose alignment editor.
+

+

Version 2.0 is the latest release + version of Jalview. This version has many new features compared to the + original version.

+

The original version of Jalview, version + 1.18, can still be downloaded. Some features no longer work.

+


+ Jalview Features -- See major new developments by trying Jalview + Version 2 --

+
    +
  • Sequence feature retrieval and display on the alignment
    • +
  • Reads and writes alignments in a variety of formats
    • +
  • Gaps can be inserted/deleted using the mouse.
    • +
  • Conservation analysis similar to that of AMAS
    • +
  • Group editing (insertion deletion of gaps in groups of sequences). +
    • +
  • Removal of gapped columns
    • +
  • Many different colour schemes
    • +
  • Alignment sorting options (by name, tree order, percent identity, + group)
    • +
  • Linking of group colours between the alignment, tree and PCA windows. +
    • +
  • UPGMA and NJ trees calculated and drawn based on percent identity + distances.
    • +
  • Sequence clustering using principal component analysis
    • +
  • Removal of redundant sequences
    • +
  • Smith Waterman pairwise alignment of selected sequences
    • +
  • EPS, PNG files can be generated for inclusion in documents
    • +
+ Authors :
+ Version 1.18 Michele Clamp; James Cuff; Stephen Searle; Geoff Barton
+ V ersion 2.0  Andrew Waterhouse; Jim Procter; Geoff Barton +

Special thanks go to Alex Bateman and the Pfam team for using Jalview + and making many helpful suggestions

+

New JalView development has been funded for three years from 1st October + 2004 by the BBSRC as part of the + "Visualisation and Analysis of Biological Sequences, Alignments + and Structures" Project. This project is coordinated by Geoff Barton + at the University of Dundee + with partners at EBI and BioSS + and consultancy (blessing :-) from Michele Clamp; the originator of + JalView.

+ +
+
+ + diff --git a/website/jalview.pdf b/website/jalview.pdf new file mode 100755 index 0000000..868b74d Binary files /dev/null and b/website/jalview.pdf differ diff --git a/website/snap22med.gif b/website/snap22med.gif new file mode 100755 index 0000000..2b6d096 Binary files /dev/null and b/website/snap22med.gif differ