-The 2.11.3 Jalview release features a new and more powerful command line interface, support for in-depth exploration of predicted alignment error (PAE) matrices from AlphaFold in the context of multiple alignments, AlphaFold's standard Blue-Orange-Red confidence colourscheme, and a host of minor improvements and bug fixes.
+The 2.11.3 Jalview release features a new and more powerful command line interface, support for in-depth exploration of predicted alignment error (PAE) matrices from AlphaFold in the context of multiple alignments, AlphaFold's standard Blue-Orange-Red confidence colourscheme, and a substantial number of [minor improvements and bug fixes](releases.html#Jalview.2.11.3.0)
**Interactive exploration of AlphaFold Predicted Alignment Error Matrices**
* 3D structure data shown in Jmol can be exported as PNG
* Scale factors and dimensions can be specified, allowing high resolution image exports
-In addition to these new functionality, next generation CLI operations can be applied to a range of files and directories through the use of wild-cards. This allows faster and more efficient processing of large numbers of alignments. It also facilitates modularisation of operations through the use of ['command-line argument files'](../features/clarguments-argfiles.html).
+In addition to these new functionality, next generation CLI operations can be applied to a range of files and directories through the use of wild-cards. This allows faster and more efficient processing of large numbers of alignments. It also facilitates modularisation of operations through the use of ['command-line argument files'](features/clarguments-argfiles.html).
All new CLI parameters are preceded by '--', as opposed to an optional single '-' which was used in Jalview's old CLI. Old style arguments can still be used, so existing scripts will still work as before, but old-style operations cannot be mixed with new operations in the same CLI call. Use of old command line operations will also raise a warning, and we plan to completely remove support in Jalview's next major release (2.12).
-As usual, please let us via [Jalview's Discussion forum](https://discourse.jalview.org) of any issues you encounter using the new CLI, and of course any requests for improvement or new functionality !
+As usual, please let us know via [Jalview's Discussion forum](https://discourse.jalview.org) of any issues you encounter using the new CLI, and of course any requests for improvement or new functionality !
git://source.jalview.org / jalview.git / blobdiff