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What's new ?
What's new ?
-Highlights in Jalview Version 2.4
+Jalview 2.6 introduces new web services, and includes an updated
+version of the Jmol molecular graphics visualization system. See the release history for the full
+details.
+Highlights in Jalview Version 2.6
- DNA and protein product highlighting
- URL links generated with regular expressions
- URL links for sequence database cross references
- New sequence fetcher dialog and DAS Sequence Fetching
- JPred Service upgraded to Jpred3
- Memory monitor
- PFAM full alignment retrieval
- Generalised sequence database reference validation
- DNA Protein Product sequence db traversal (Experimental)
- VAMSAS Interoperation Client (Experimental)
- export annotation rows as CSV for spreadsheet import
- New application command line args and optional Groovy suport
- New Applet API methods and parameters
+ - JABA Web Services for
+ multiple alignment using:
+
+ - ClustalW
+ - MAFFT
+ - Muscle
+ - ProbCons
+ - T-COFFEE
+
+
+ - User modifiable alignment service parameters
+ - Visualization of superposed structures associated with protein
+ or nucleotide sequence alignments.
+ - Export coordinates and projection as CSV from PCA viewer
-Issues Resolved (a select list)
+
+Issues Resolved (a select list - see release history for details)
- Aligned cDNA translation to aligned peptide works correctly
- selected region output includes visible annotations (for
- certain formats)
- edit label/displaychar contains existing label/char for
- editing
- Newick tree support improved for clustalW trees and preserving NHX style comments
- Pathological filechooser bug avoided by not allowing
- filenames containing a ':'
- Fixed exception when parsing GFF files containing global
- sequence features
- Reference counting for alignment datasets
- better reporting of non-fatal warnings and error messages to user when file
- parsing fails.
- Save works when Jalview project is default format
- Histidine should be midblue (not pink!) in Zappo
- Undo recovers dataset sequence metadata when sequence
- regions are cut
- PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) are read in properly
- Stockholm annotation parsing fixed and improved (PFAM records)
- Re-instated Full AMSA support and .amsa file association (MyHits)
- annotation consisting of sequence associated scores can be
- read and written correctly to annotation file
- Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet
- Applet Menus are always embedded in applet window on Macs.
- Newly shown features appear at top of stack (in Applet)
- Secondary structure lines are drawn starting from first
- column of alignment
- Uniprot XML import updated for new schema release in July 2008
- Sequence feature to sequence ID match for Features file is case-insensitive
- Sequence features read from Features file appended to all sequences with matching IDs
- PDB structure coloured correctly for associated views containing a sub-sequence
- Display name and local features preserved in results retrieved from web service
- Visual delay indication for sequence retrieval and sequence fetcher initialisation
- Updated Application to use DAS 1.53e version of dasobert DAS client
+ - clustalx colourscheme colours Ds preferentially when both D+E
+ are present in over 50% of the column
+ - Prevent sequence fetcher from replacing ',' for ';' when querying DAS sequence sources
+ - InstallAnywhere builds fail to launch on OS X java 10.5 update
+ 4 (due to apple Java 1.6 update)
-
-
See the Release History page for
details of all new features and resolved issues.