X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=297233de91dd97a110bee36910d925156a9e8441;hb=9ee29162e3f41c2a60c50f1fda2f3d045adb658f;hp=d124cc8d5de3e7904164dc87fd7fd9e7f48271db;hpb=9a881df532ecf49063d4f032144533b9a1a89319;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index d124cc8..297233d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,63 +24,120 @@

- What's new ? + Jalview 2.10.2b1 bugfix release

- Jalview 2.9 has been in development since December 2014. In addition - to a multitude of bug fixes and minor improvements (both small, and - rather big!), it also brings major new capabilities for codon-level - analysis of protein alignments and the manipulation of structural - data.
For the full list of changes, see the Jalview 2.9 Release Notes. + This is patch release for 2.10.2. See the release notes for full + details bugs addressed in this version, which also introduces + additional improvements to the overview panel, and patches for + several minor issues including the ability to correctly recover + cross-references for Uniprot protein sequences from Ensembl.

- Highlights in Jalview 2.9 - + What's new in Jalview 2.10.2 ? +

+ Version 2.10.2 was released in August 2017, and introduced new user + interface features, improved and more extensible tree and PCA + analysis, more robust 3D structure viewing with UCSF Chimera and an + updated service client for JABAWS. The full list of bug fixes and + new features can be found in the 2.10.2 Release Notes, but + the highlights are below. +

New dialog and faster and more + configurable Tree and PCA calculations
Menu entries for + calculating PCA and different types of tree have been replaced by + a single Calculations + dialog box. The underlying implementation for the PCA and tree + calculations have been made faster and more memory efficient.
Extensible score models
A new + framework has also been created for the score models used to + calculate distances between sequences and shade alignments. This + framework allows import of substitution matrices in NCBI and + AAIndex format.
PCA Bug Fixes. Jalview's + implementation of PCA differed in its treatment of gaps and + non-standard residues. The BLOSUM62 matrix also included a typo + that affected results. See the 2.10.2 release note + about score model bugs for details and how to reinstate legacy + behaviour.
Update to JABAWS 2.2
Jalview's + alignment, protein conservation analysis, and protein disorder and + RNA secondary structure prediction services are now provided by JABAWS 2.2. + Several of the programs provided as JABAWS 2.2 services have been + updated, so their options and parameters have changed.
URL linkouts to other bioinformatics + databases
New preferences for opening web pages for + database cross-references via the UK Elixir's EMBL-EBI's MIRIAM + database and identifiers.org services.
Showing and hiding regions
Hide insertions in the + PopUp menu has changed its behaviour. Prior to 2.10.2, columns + were only shown or hidden according to gaps in the sequence under + the popup menu. Now, only columns that are gapped in all selected + sequences as well as the sequence under the popup menu are hidden, + and column visibility outside the selected region is left as is. + This makes it easy to filter insertions from the alignment view + (just select the region containing insertions to remove) without + affecting the rest of the hidden columns.
Gap count - a.k.a. the Occupancy + Annotation Row
Another way to filter columns according to + the presence of gaps is to enable the Occupancy + Annotation row via Jalview's Preferences. This annotation row + shows a histogram of the number of aligned residues at each + column. The Select + By Annotation dialog now also includes a percentage threshold + mode, to make it easy to filter alignments to show only those + columns with a particular fraction of aligned sequences.
Recent search history for Find, PDBe and + Uniprot
Easily repeat a previous search for Find and the free + text search system (for querying Uniprot and the PDBe).
Improved Overview Window
The alignment overview is now easier + to use when working with alignments of more than 5000 rows and + columns, and features a new pop-up menu that allows hidden regions + to be excluded from the overview. It also works with CDS/Protein + alignments and MSA views in wrapped mode.
3D Structure
Jalview's communication + with UCSF Chimera has been made more robust, particularly when + working with many structures and long sequences. Regions in + structures that correspond to hidden regions in an alignment view + are now left un-coloured, making it easier to highlight specific + features in 3D. See below for experimental + features for exchanging annotation between Chimera and Jalview.

+ Scripting
New groovy examples + demonstrate Jalview 2.10.2 APIs for creation of data-driven + colourschemes, and custom alignment file handlers. The FeatureAnnotationWorker + introduced in Jalview 2.10 has also been refactored to allow + efficient counting across multiple feature types. Please be aware + that feature counter scripts created for earlier versions will not + execute in Jalview 2.10.2. +

+ Experimental Features +

+ This release of Jalview introduces an Experimental Features + option in the Jalview Desktop's Tools menu that allows you + to try out features that are still in development. To access the + experimental features below - first enable the Tools→Enable + Experimental Features option, and then restart Jalview. +

Visualisation, editing and analysis of - cDNA and Protein alignments
A new Split View window allows linked - protein and nucleotide sequence alignments to be viewed, edited, - and analysed as one.
cDNA alignments can also be - reconstructed from protein alignments calculated by Jalview's web - services, and update in response to edits in the amino acid view.
To - start experimenting with cDNA/Protein analysis, jut drop a file - containing cDNA sequences which code for, and have IDs matching - proteins in an existing alignment, and Jalview will do the rest.
Enhanced Integration of UCSF Chimera
Jalview - 2.9 provides full support for the use of Chimera to view 3D - structures linked to alignment views in the Jalview Desktop. We've - also included support for saving Chimera sessions in Jalview - project files.
Jalview and Chimera communicate using local - web server connections, which may cause firewall alerts on some - systems, but has the advantage of allowing bidirectional - communication. Communication between Jalview and Chimera is now - much more responsive, and selected regions in Chimera are now - shown as highlighted regions in the Jalview desktop.
Interactive querying of the PDBe
Jalview - users can now browse and retrieve 3D structure data from the PDB - via the PDBe - Search API (Gutmanas - et al 2014). Developed in collaboration with the PDBe group at - EMBL-EBI, the interface allows both structured and free-text - queries to be performed, and allows automatic selection of the - most relevant structures for an alignment acording to a variety of - criteria.
Improved support for RNA visualisation
Jalview - 2.9 integrates the latest version of the VARNA RNA Viewer, and VARNA views - can also now be stored in Jalview projects. We've also dealt with - a number of lingering bugs in the VARNA/Jalview interface, - including the loss of pseudoknots when RNA secondary structure is - shown VARNA.
Protein Secondary Structure predictions - with JPred4Jalview includes a number of new features for working - with secondary structure predictions from the JPred4 server. These - include the ability to automatically hide insertions and highlight - mutations in an alignment with respect to a reference sequence. - Jalview 2.9's new scrollable SVG HTML export mode was also - developed specifically for the JPred4 server.
Annotation transfer between Chimera and Jalview
Two + new entries in + the Chimera viewer's Chimera menu allow positional annotation to + be exchanged between Chimera and Jalview.