Index of /aliview/downloads/linux/beta

Icon  Name                                 Last modified      Size  Description
[PARENTDIR] Parent Directory - [   ] 2019-04-07 15:07 3.7M [   ] AliView-1.26.jar 2019-04-07 15:28 2.4M [   ] aliview.jar 2019-04-07 15:35 2.6M [DIR] linux-version-1.19-beta-2/ 2016-08-04 08:46 - [DIR] linux-version-1.19-beta-3/ 2016-08-23 09:16 - [DIR] linux-version-1.19-beta1/ 2016-03-23 20:48 - [DIR] linux-version-1.19-beta1a/ 2016-03-25 08:37 - [DIR] linux-version-1.19-beta1d/ 2016-03-25 16:57 - [DIR] linux-version-1.19-beta1k/ 2016-05-03 06:43 - [DIR] older_beta/ 2016-03-09 15:02 -
Version history


- Big rewrite of code handling selection. Improvements and more standardized mouse selection of sequences (compared to other software)
- Fixed bug when saving alignment in Phylip format with "Save" command, padding was lost.
- Improvements when translating nucleotide sequences into aminoacid - editing sequences are now fully supported.
- Selection follows when translating sequences
- Added capabilities to define,edit, export(in RaxML format) and view Charsets in alignments
- Added "Show both aminoacid and nucleotide sequence" when translating nucleotide sequences to amino acids
- Added "slow" double click on name as a trigger for renaming a sequence
- Mouse wheel zoom in and zoom out is also working when mouse pointer is on sequence list
- Dropping an alignment file can now be done anywhere on the alignment program
- Quicker scroll when dragging sequences outside visible part of list
- Big rewrite of code handling large files (> 1GB)
- Improved multithreading in some sections of program makes it even more responsive.
- Fixed bug on Mac where sequences sometimes were saved in temp directory without asking user 


- Fixed error in invertebrate mitochondrial coding table TGA was not coded as STOP, all other coding tables were verified without errors.


- Fixed bug that made it impossible to close error message if something went wrong when aligning
- Duplicate sequence names are being selected in alignment at startup
- Adjusted simplified nexus format, it now replaces all non alfanumeric characters with _ in the sequence name, keeps only (A-Z a-z 0-9)
- It is now possible to find and select duplicate sequence, "Edit" | "Find and select duplicate sequences"  (this function is still beta)


- Added shortcut Command/Ctrl + W (for closing window)
- Added function "Upper case" under View menu
- Added undo functionality when renaming sequence name
- Less padding after sequence names when saved in Nexus codonpos-format
- Fixed bug affecting saving in Nexus codonpos-format after deleting columns
- Fixed bug in function Expand selection right
- Added function "Add new empty sequence"
- Added "Rename sequence" to right click menu
- Fixed bug where "Align everything" did not stop if cancel button was selected
- Corrected viewing position when switching between "Translate one pos aminoacid" and nucleotide view


- Fixed bug in "count stop codons" function
- Fixed bug where translation into Aminoacids sometimes not included the end of the alignment
- Fixed bug on Mac OS X Yosemite and Mavericks and latest java JRE that caused program not to start 
- Unwanted blanks are trimmed away at start and end of text pasted into the search field
- Unwanted blanks are trimmed away at start and end of clipboard text in function "Reverse complement clipboard"
- Removed function "Invert selection"
- Added functions "Expand selection Right" and "Expand selection Left"
- Added shortcut keys to menus (Mnemonics)
- Small change in how shift selection works
- Selection is displayed in info-panel after performing a Find/search
- Small improvement in "Recent files" handling
- Fixed bug where Excludes did not move when whole column was deleted


- Fixed bug on Windows that caused message window always to be on top when running external commands
- Changed message window not to be on top of other programs when running alignment programs on Linux
- Now possible to hide "Allow edit" dialog
- Info message if alignment contains duplicate sequence names 
- Adjusted status panel, selected position is now zero before first non gap residue
- Changed header slightly when saving in Clustal format


- Fixed bug when realigning a selected block of residues


- Fixed issue with screen tearing on Linux versions running Open-JDK
- Fixed issue with pixelation on Mac retina-screen
- Fixed issue with tooltips on Linux versions running Open-JDK


- Drawing speed improvements on Windows associated with the List of sequence names 
- Fixed problem when translating some alignments to AminoAcid one pos
- Added last saved file to "Recent files" menu
- Added "Save as Phylip (relaxed, padded & interleaved)" option
- Corrected some non standard implementations when reading and saving in phylip format
- Now replaces gap symbol '.' with '-' in input alignments
- Added information message to user if the size of the alignment panel window is larger than 2147483647 pixels
- Adjusted columns in the status panel at bottom
- Fixed so that selection now is cleared in list after deleting sequences
- Fixed some issues with occational "tearing" of the alignment view when zooming out in version 1.10


- Improved render speed (5-10 times!)
- Added save alignment as strict 10 char sequential Phylip format
- Added undo/redo support when sorting sequences with functions "Sort sequences by...."
- Fixed problem when re-aligning selected sequences only
- Fixed problem rendering sequences that was longer than 100 million bases (e.g. human chromosomes)


- Added format support for CLUSTAL(.aln) and MSF
- Added "Save fasta index file" functionality
- Revised the Nexus format output
- Revised the Phylip format output and input
- Improved error dialogs so that they are no longer hiding each other.
- Fixed bug where the * symbol did not disappear from window although the file was saved
- Fixed bug where "Delete vertical gaps" did not work if the first column was all gap
- Fixed drag drop function where dropped sequence sometimes were positioned one position to low
- Changed version menu item to "Check for new version/version history"
- Added button "Count stop codons" on translate sequence toolbar
- Added info message if MUSCLE profile algorithm is used for adding sequences


-Fixed error in Mac-version where all Menus got greyed out after alignment program error
-Fixed key repeat problem in Linux and Java 8
-Fixed problem where "Recent files" menu not always got updated
-Fixed problem with cursor not stopping at edge of alignment
-Improved drawing speed when translating nucleotides
-Fixed color problem when selecting and "Highlight consensus/non-consensus/trace"
-Changed "Add-Remove selection to Excludes" so that it now toggles add/remove selected chars - with same shortcut key
-Added "Delete gap at right" - functionality
-Added function "Ignore gaps when translating"
-Changed color theme (Default-faster) and (SeaView), selected character are less different - makes manual alignment easier
-Added "Sort sequences by char in selected column"
-Added Menu "Count stop codons"
-Added message when no primers were found in selected region (instead of just silently do nothing).


-Fixed "Out of Memory" problem when editing some large datasets, the problem was that the Undo function was draining all memory
 resources on very large files. Now Undo functionality is turned of before memory error and user is notified
-New dialog that notifies user about low possible memory problem if keeping to many large alignments opened at the same time.
-New menu item "Check version history" in Help menu

-Error handling and error message if you are using 32bit Operating system and
trying to open large files


-Different color on gap and matching characters in "Highlight differences" mode
-Improved error handling if unable to load or save files


-Fixed issue "Cursor movement at edge of pane is making whole pane scroll"


-Added version check menu item


-Improved error message handling