GeneDoc release 2.2 (Freeware for Windows)

Ketchup Ketchup at CRIS.COM
Fri Oct 31 11:37:28 EST 1997


Greetings All, 

Please be informed that GeneDoc version 2.2 has been released to 
the GeneDoc web site. 

http://www.cris.com/~ketchup/genedoc.shtml

GeneDoc is freeware for PC/Alpha/Windows/3.1/95/NT

This version has many bug fixes and some fun new features. 

GeneDoc can now parse ProSite/ReBase files and find and shade motifs 
in your alignment. You can manually edit/add to the motif list as well.

An output to HTML option has been added that works very nicely. 

GeneDoc can write a RasMol coloring script, so that you can apply
GeneDoc 
shading in RasMol, as well an option to display sidechains for a 
selected set of colors. For example a script could put conserved 
mode shading onto a protein, set the display to ribbon mode and show 
sidechains where the alignment was 100% conserved.

More control over the amount of the sequence names to be displayed and 
other parts of the display has been added.

GeneDoc now parses, saves and displays branch and node weights from 
phylogenetic tree files.

The GeneDoc information in the header of the .MSF file has been changed 
and looks a lot better and is safer.

The complete list is appended below.

Once again, a great deal of changes and bug fixes are from user 
feedback. Thanks for all the kind words, support and suggestions.

Karl Nicholas.

--------------------------------------------------------------------
2.2
* Fixed 'Clear all Gap Columns' Function.
* Added AutoJustify of Max Name Length and Max Position Indicator
Length.
* Added Max Name Length Displayed Field.
* Added User Configured Name/Sequence Block seperation string.
* Added User Configured Seq Loc Ind/Sequence Block seperation string.
* Added Phylip File Import function.
* Fixed program hanging when doing File/New, File/Import,
  and then a caret positioning function.
* Fixed program crashing when deleting all sequences.
* Added UnOfficial CrossHatch pattern support for background shading.
* Added ability to select Sequences to be exported.
* Changed the GeneDoc information section of the .MSF file.
  *** NOTE: This new header can NOT be read by previous versions of
GeneDoc
* Added ProSite/ReBase Search Results mode.
* Added Auto-Load Search Lists with ProSite or ReBase files.
  List gets loaded with matches found in the ProSite or Rebase Files.
* Fixed the Copy to New Project function in many cases, most having
  to do with group information being copied.
* Changed Structure Sequence Matching rountine to work for both
  overlap and within cases.
* Added HTML output.
* Added RasMol coloring script output.
* Added Weights in Phylogenetic tree parsing.
* Fixed page up bug.
* Fixed Pict files sequence names not being group colored.
* Relaxed .MSF input routine, does not need spaces every 10 in data
rows.
* Fixed import routines to get last char if no last CR/LF.
* Added RasMol SideChain display options to coloring script output.
* Changed Duplicate Sequence Names To Complain and Notify, but not
abort.
* Changed Group Names in Group Sequence Dialog to be colored with
  group colors.
* Changed Fasta input to limit names to length of 20.
* Added conserved shading of substitution groups styles. 
* Fixed extra CR/LF being added to comments in file with each additional
file save.




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