Change log

Donate and contribute to the PlasmidTools project

PlasmidTools Wpf

2.6.3.0 (2022-03-12)
Fixed a couple of errors in the user interface:
- When closing all projects and the Hairpin analysis was open, the Multi-purpose pane showing the analysis was not closed. Fixed.
- When closing all projects and the Annotation Manager was open, a warning message was displayed. Fixed.
Web pages:
- Web pages related to installation/upgrades/migration/potential installation issues have been updated to comply with recent changes.

2.6.2.0 (2022-02-20)
- When saving the list of annotations in the 'Annotation Manager' and the project sequence contained a pair of annotation brackets (<...>) at the very end, an 'Out of range' exception was thrown. Fixed.

2.6.1.0 (2021-07-10)
- Fixed a connection error popping up when running the 'Ckeck for updates' and 'Update restriction enzymes' functions.

2.6.0.4 / 2.6.0.5 (2020-06-05)
- Fixed a problem in the 'Sequence Database manager' in which the annotation type 'Region' was automatically assigned the value 'No direction' when saving changes in a database file.
- Changes in the user interface: function-specific parameters and settings moved from main toolbars to self-contained analysis windows in the multi-purpose pane.
- Added a new function to map hairpin (stem-loop) structures in single-stranded RNA/DNA.
- Added additional options to the 'Create optimized ORF' function: 1) skew codon usage away from rGTP- and rCTP-containing codons to reduce secondary structures, 2) choose between three levels of magnitude when skewing codon usage to reduce rGTP- or rCTP/rGTP-containing codons.
- Oligo primer analysis: modified how primer search ranges are set initially. If a subsequence is selected in the sequence editor before starting analysis, primer search ranges are confined to the adjacent 100 bp on each side of the selection. If nothing is selected, search ranges are the first and last 100 bp of project sequence. Search ranges are of course adjustable.
- Fine-adjustment in molecular-weight calculations of DNA/RNA.
- Fixed display of codon-usage tables when opened in Text editor.

2.5.0.0 (2020-04-05)
- Text editor has been converted into a rich-text editor with headings and formatted text. Results and reports created by PlasmidTools are displayed as rich-text documents. Documents can be saved as rich-text (*.rtf) or plain-text (*.txt, *. genbank, etc.). Print functionality is also implemented.
- Project tabs display a 'star' indicator when project has unsaved changes.

2.4.0.2 (2020-01-16)
- Fixed an error introduced in version 2.4.0.0 that added blancs to the end of sequence names (shown in the toolbar) in opened projects.

2.4.0.0 / 2.4.0.1 (2020-01-16)
- Added interactivity between graphical map and sequence editor. Left-click on a map element and the corresponding sequence becomes highlighted in the sequence editor. Very useful to locate subsequences and positions in the editor.
- Added an alternative mode for refreshing graphical maps and behind-the-scenes data when typing in the sequence editor: 'On demand', in which refreshing is suspended until pressing the ENTER key. This may be useful on slow computers when editing very long and complex sequences having numerous annotations, to avoid lagging and seeing strange map rearrangements while typing. Standard and default refresh mode is 'Immediate' in which graphical maps are refreshed after every keystroke. Refresh mode is selected in the Options menu.
- Added close buttons to sequence tabs.

2.3.0.0 (2019-09-29)
- Added a new function for creating optimized open reading frames (ORFs) for expression in selected species. There are options to modify codon usage for in-vitro transcription with Cap nucleotides, in which rGTP concentration is limiting, and for excluding rarely used codons. The source sequence may be DNA, RNA or protein.
- Upgraded the "Codon usage analysis" function. It now shows statistics for the actual codon usage of the different codon triplets, compared to optimal codon usage in the selected species.
- Fixed an issue with the "Primer report" function in "Primer analysis" which could crash on rare primers having a round integer value for Tm (decimal rounding error).

2.2.0.0 (2019-08-18)
- Implemented a third type of region annotation intended for open reading frames. The new type has its own color in graphical maps and is denoted by "++" (forward direction) or "--" (reverse direction) in annotation text. To apply the new region type to existing annotations, open the 'Annotation manager' and select 'Orf' as type. Sequence database entries created in earlier versions may be set to '"Orf" in the 'Sequence database manager'.
- Redesigned color pickers for circular/linear maps. The implications of color changes with respect to other background and foreground colors are now explicitly displayed in the color picker. Changes are no longer saved instantly to graphical maps, but when the 'Save & close' button is clicked. A new 'Cancel' button may be used to cancel the operation.
- The 'Annotate selection' function caused the 'Sequence editor' and sequence tabs to freeze and not display selected seqence. Fixed.

2.0.9.0 (2019-06-17)
- Menu-item icons had incorrect size on Windows 7 machines. Fixed.

2.0.8.0 (2019-06-09)
- Graphical improvements in the user interface.
- Correct start position in 'sequence/translation combined view'.

2.0.7.0 (2019-06-05)
- Added many new species to 'codon-usage compatibility analysis'.

2.0.6.0 (2019-05-26)
Linear map:
- The vertical positioning of map elements now adjusts to the complexity present above and under the sequence line.
Sequence alignment:
- New function to add a sequence to the alignment by pasting the Windows clipboard contents (standard copy - paste). Use the toolbar button 'Add from clipboard'.
- When doing manual edits in the alignment the alignment editor lost focus (cursor disappeared) for every change made. Fixed.

2.0.5.0 (2019-05-06)
- The different panes/sections in the user interface (sequence pane, multipurpose pane, graphical map) have become resizable. Resizing is done the usual way: hoover over an internal border to bring up the resize handle, click and drag to resize.
- Annotation manager: cell contents could not be edited. Fixed.
- Primer analysis: if a results table had only one result (row), clicking on the result did not highlight the corresponding sequence in the sequence pane. Fixed.

2.0.4.0 (2019-03-19)
-The translate to protein functions 'Translate from cursor' and 'Translate selection' have been merged into a single function: 'Translate to protein'. If a subsequence is selected in the sequence pane, translation will be confined to the selected region. If nothing is selected, translation will start at cursor position and proceed to the first in-frame stop codon.
-Added a function to display a combined view of nucleotide sequence with protein translation beneath (Analysis menu > Sequence/translation combined view). If a subsequence is selected in the sequence pane, output will be confined to the selected region. If nothing is selected, output will start at cursor position and proceed to the first in-frame stop codon.
- Added a new function for copying sequence in the sequence pane that deletes annotation text and brackets before sending it to the clipboard (Edit menu > Copy sequence only).

2.0.3.0 (2019-03-08)
-If a new session was started, and only linear sequence(s) were opened, the 'Search for subsequence' function caused a rearragment of the user interface, because the results table was docked in the toolbar.
-When showing results from 'Search for a subsequence' or 'Restriction site analysis', and the results table had only one result (row), clicking on the result did not highlight the corresponding sequence in the sequence pane.

2.0.2.0 (2019-03-03)
-Installation method changed from online to stand-alone (downloadable) installer. The stand-alone installer is signed with a self-signed certificate, which means that Windows will say 'unknown publisher' during installation. However, the installer is still signed with an encrypted key and protected against tampering.
-Added vertebrate mitochondrial DNA as a new sequence type (mtDNA). Mapping of open reading frames and translation to protein in mtDNA has modified rules compared to standard code: ATA is methionine (M) and additional start codon; TGA is tryptophane (W).
-Added a new function for translation to protein: 'Translate selection' (translate sequence selected in the sequence pane). This may be useful when translating mitochondrial genes, since many have incomplete stop codons.
-Import of GenBank and EMBL sequences now handles rRNA and tRNA gene annotations.

2.0.1.0 (2018-01-29)
- Rewamped graphical maps with higher resolution and more space-efficient layout.
- Added Undo/Redo functionality to project sequences.
- Removed some empty tooltip boxes popping up in the user interface.
- Added recommended hybridization temperature as a new field in the "Oligo primer report" to emphasize that Tm is not the same as hybridization temperature (this is explained in the manual).

2.0.0.6 (2017-11-21)
Cloning Tool:
- The two sequences (fragment tables) used in cloning can both contribute a vector backbone to a new construct and thereby set plus strand and zero position. It could then be confusing that the two buttons for opening files were labelled "Donor" and "Recipient". They have been replaced by standard file-open buttons above each table.
User interface:
- When closing all open projects, and the last project closed was circular, and then open stand-alone functions like Cloning Tool and Database Manager, the user interface did not rearrange correctly.

2.0.0.5 (2017-11-09)
- First release of the new PlasmidTools Wpf application, a fully compatible replacement for PlasmidTools Net40 which has been discontinued.

PlasmidTools (Net40)

1.4.0.1 (2017-11-09)
- Final version of PlasmidTools Net40. Users should make the transition to PlasmidTools Wpf.

1.4.0.0 (2017-06-05)
Cloning Tool:
- Restriction-enzyme- and Gateway cloning have been separated into two different modes of operation. The mode is set in the toolbar. When mode is set to restriction enzymes, only restriction enzymes are shown in the enzyme list. When mode is switched to Gateway, only Gateway sites are displayed, and all sites are initially selected to accomodate best practice.
Restriction site analysis:
- Gateway sites have been removed from restriction-site analysis, where they strictly do not belong. Gateway sites are mapped through database scanning and used in cloning when this mode of operation is selected in the Cloning Tool.
- Added two new categories to the restriction-enzyme filter, 3' overhang and blunt cutters.
- The restriction-enzyme update function could not download new definitions due to a change in NEB's access policy. The definitions are now obtained from another web site.

1.3.11.0 (2017-05-28)
Annotation manager:
- Added an option to delete all annotations for a specific restriction enzyme when one is selected and deleted. The mode of operation is set in the Annotation manager's toolbar (toggle switch on the right side), and is ON by default. The search for identical restriction-enzyme sites is based on annotation names, so the annotations must have the original restriction-enzyme names inserted by restriction-site analysis in order to be detected.
- When copying annotations to the currently selected target sequence database, and that specific database is open in the Database Manager, the annotations are now added directly to the database table in the Database Manager. (In previous versions it was saved directly to the database file, which could then become overwritten when saving the file in the Database Manager).
- Removed flickering in the sequence editor when several annotations were deleted in batch operation.
Open reading frames (ORFs):
- Optimization of algorithms. Increased speed in translation to protein and mapping of ORFs, in particular when mapping ORFs in long sequences.
Restriction enzymes:
-  The function to download and update restriction-enzyme definitions now opens in a separate window (module). The main program will then not be affected in case of a slow connection or interrupted download.
- Some restriction-enzyme annotations could be wrongly mapped when switching strands (reverse complement). This would happen in the special situation when the restriction enzyme belonged to one of the optional enzyme categories, and this category was not selected to be used in analysis at the time of switching strands. The annotation was not detected as being an enzyme cut site and the overhang was not considered when calculating position on the opposite strand. (a second strand switch would bring it back in correct place, though). All restriction enzyme cut sites are now detected as such, regardless of which enzyme categories are active.

1.3.10.1 (2017-04-04)
- Optimization of program code and algorithms. Increased responsiveness in many functions. Considerably faster when editing long sequences.

1.3.9.0 (2017-02-15)
Sequence alignment:
- Import of sequences to be aligned with a reference sequence ('Add sequence' button) now supports batch import of multiple files. In the open-file dialog, Ctrl-click to select specific files, or click and Shift-click to select a range of files.

1.3.8.0 (2016-12-28)
Annotations:
- Added a new method for annotating subsequences. Annotations are usually added from analysis and search results by clicking the Annotate button, or by filling in a new row in the annotation manager including start and end positions, or by manual editing in the sequence editor. It is now possible to annotate a sequence range directly in the sequence editor by selecting a range and then choose the 'Annotate selection' menu item in the right-click or top menu.
Oligo primer analysis:
- Added information about filtering events and how many primers passed each test. This will make it easier to judge which parameter(s) to adjust when adjustment is needed, for example if few or no primers are listed. To view filtering data right-click in a primer table and select "View filtering events".
- The default range of allowed 3' dG values has been lowered a little (increased affinity), from [-2.9, -4.1] to [-3.1, -4.2].
Sequence editor:
- Some editing functions did not present an explanation when the requested edit was blocked because the sequence editor was in read-only mode, which happens when the results pane or annotation manager is open.

1.3.7.0 (2016-12-07)
Oligo primer analysis:
- Added molecular-weight information for primers in the "Primer report".
User interface:
- Added unit of measurement for temperature and free energy where it's reported.
Sequence pane:
- Imported sequences no longer have pre-entered filenames (since it could look like it was allready saved to file, which it isn't).
- When undoing operations by loading the last set restore point the project is no longer marked as changed.
- When a pair of annotation brackets (<>) was inserted by using the right-click menu it didn't stick unless text was added inside. The brackets are now saved anyway.

1.3.6.1 (2016-11-21)
Sequence pane:
- When typing sequence in the sequence pane (keyboard input) the last character typed was not registered, unless other modifying functions were run afterwards. The bug has been there since version 1.3.2.1 (2016-06-23).

1.3.6.0 (2016-11-20)
Properties window:
- The sequence properties info window can now display properties of a selected subsequence if one is selected in the sequence pane. If no subsequence is selected the properties apply to the entire sequence.
- The amount of information has been extended. Regardless of sequence length the properties window now includes molecular weight and melting temperature. For sequences shorter than 50 the info also includes 3' delta G, 3' dimer delta G and internal dimer delta G, including visual representations of the most stable primer-dimer interactions.
Sequence alignment:
- The "Window" parameter is no longer read in real-time while being typed in, which caused an error message to pop up if the number was deleted before typing a new value. It is now read and checked when the align and re-align functions are activated.

1.3.5.0 (2016-11-04)
Sequence database scanning of project sequences has been modified to detect imperfect matches. The function reads the "Minimum sequence identity threshold" value in the toolbar pane, which it shares with the sequence search function.

1.3.4.1 (2016-10-12)
The demo project available in the help menu failed to open.

1.3.4.0 (2016-09-11)
The sequence search function has been modified to detect imperfect matches. A minimum sequence identity threshold may be set in the main toolbar beside the search button.

1.3.3.1 (2016-08-18)
Sequence database functionality and scanning has been redesigned to operate directly with database files on disk:
- The sequence database manager has become a place to open and edit different database files and is no longer restricted to save the "CustomSequenceDatabase" file only.
- Added functions to copy and paste database entries from one database to another via a special database clipboard.
- Added a new filtering function (Sequence Db menu) to select which database files are used in scanning. The available files are those stored in the "PlasmidToolsData" directory.
- Added a new function to select which target database file will receive new entries when using the "Add to database" function in the annotation manager. The target database may be set in the annotation manager and the Sequence Db menu.
- Added the antibiotic resistance genes and Gateway recombination sequences as customizable database files in the "PlasmidToolsData" directory.
- The scan function now reads database entries directly from files while scanning to minimize the use of system resources.

1.3.2.1 (2016-06-23)
Sequence editor:
- An unmodified project sequence could mistakenly be marked as modified, causing a save-or-not dialog to pop up when closing the file.

1.3.2.0 (2016-06-14)
Sequence database:
- Changed the method for saving the custom sequence database. In previous versions it was saved internally along with program settings. It is now saved in a separate file and folder. Having a separate storage location for the database will ensure its integrity when future program updates are installed or the application is reinstalled. The database file and folder is set up on first application run, and may be changed later using the new "Sequence database setup" procedure (SequenceDb menu).
User interface:
- Several program modules have got separate memory of the last accessed folder, including the Cloning Tool, Alignment Editor (separate for alignment files and sequence reads), Text Editor and File-Import.
- Some cleaning up and rearrangements in the menu.

1.3.1.1 (2016-04-13)
Sequence database manager:
- The ID (name) in the first row could be invisible (empty) after replace/import of a sequence database.

1.3.1.0 (2016-04-10)
Sequence database manager:
- Moved the functions for export and import of custom databases to the Sequence Db Manager, where they better belong. The content of the database is then visible and editable where the export/import is done.
- Added a  new function to merge a database file with the current active database.
- Added a new close button for closing the manager, which is aware of unsaved changes and in case presents proper options.
- The database backup file (../My documents/PlasmidTools_SeqDb_backup) is now saved every time the active database is saved (previously this happened when the program was closed). If the database becomes replaced after program update or re-install the backup file will in any case contain the database last saved in the database manager (also after repeated program start-close events).

1.3.0.2 (2016-04-04)
Annotation Manager:
- The Annotation manager did not allow manual editing in table cells. This is now back in order.
- Used the opportunity to add a choice to save or not when closing the annotation manager and it contained unsaved changes.

1.3.0.1 (2016-04-03)
Sequence editor:
- The "convert to uppercase/lowercase" functions can now be applied to a selected range of nucleotides, if a range is selected. If nothing is selected the case is applied to the whole sequence. Annotation text is not modified.
- Removed an annoying flickering in the sequence pane when the results pane was opened or closed.

1.3.0.0 (2016-03-28)
Sequence editor:
- Removed the automatic insertion of an annotation right bracket (>) after a typed left bracket (<). It required extensive monitoring of keyboard input, which was not compatible across all keyboard layouts and language settings.
- Removed a number of warning messages given when the sequence was edited and contained empty or unpaired annotation brackets. Instead, program functions have been modified to deal with such errors, and pop-up warnings have been limited to situations in which the integrity of the project sequence is at risk or analysis results will be erroneous.
Switch strands (reverse complement):
- The function no longer converts the project sequence to uppercase, but preserves the case of each nucleotide.
- Non-nucleotide characters are not modified, and unpaired annotation brackets are switched.
Sequence Database:
- Added a backup file of the sequence database. It is saved in the user's root folder ("My documents" on English OS) each time the program is closed. To restore the sequence database from the backup file, use the "SequenceDb - Import Db file" function.

1.2.7.0 (2016-03-13)
- Added a new function to update the restriction enzyme database to the latest version found in ReBase. Also added a function to restore the database to the last built-in version (which at present is 602 (01-2016)) in case a downloaded update should be corrupted (which does not happen often). The functions are found in the "Resources" menu.

1.2.6.2 (2016-02-28)
- Latest version of the GCG restriction enzyme database.
- Fixed a syntax error that could cause problems with PlasmidTools file-type association and double/right-click functionality in Windows Explorer. The fix may not take effect when updating an existing installation on a computer running a recent version of Windows. For further information about the issue and how to fix a broken file association, read this.

1.2.6.1 (2016-02-21)
User interface:
- Added additional information in the toolbar about what is selected in the sequence pane. The top-most field ("Selection") shows the selection range if a range is selected, or the cursor position if nothing is selected. The field below ("Length") shows the length of the selection, or "0" if no range is selected.
- The selection status in the different project sequence tabs are now remembered and visible when switching between tabs.
Codon-usage compatibility analyis:
- Added Gallus gallus (chicken) and Xenopus laevis (African clawed frog) to the analysis.

1.2.5.0 (2016-02-14)
Restriction site mapping:
- In the special situation when a restriction enzyme that cuts outside the recognition sequence was detected to cut the plus-strand on the very 5' or 3' end of a project sequence defined as being linear, the position was still being scored as a hit, although this cut only could happen in a circular sequence.
- Some other fine-tunings for handling restriction-enzyme cut sites at the ends of linear sequences.
Switch strands (reverse complement):
- In the special situation when an annotation for a restriction enzyme that cuts outside the recognition sequence was present close to the end of a linear sequence, and the strands were switched (reverse complement), the plus-strand cut position could end up outside the linear sequence, and the program aborted the operation. Such cut-site annotations are now removed and a message about the issue is displayed.
Sequence alignment:
- The length of the search window used by the aligning algorithm to establish a match is now customizable. The sequence alignment editor can then be used with short sequences, for example to check complementarity between oligo-nucleotides when designing linkers.

1.2.4.0 (2016-01-31)
- Help content and some other info messages are now opened in resident windows that can stay open side-by-side other windows where the work is done.
-When the sequence pane is locked for editing (due to the results pane or annotation manager being open), a message about this is displayed when trying to edit the sequence.

1.2.3.0 (2016-01-23)
- Up-to-date restriction enzyme database.
- Introduced a distinction between the two cut sites made by restriction enzymes that cut twice. The recognition sequence may be non-palindromic and the offset (distance) on the two sides may be different. In restriction enzyme databases such enzymes are listed twice, one for each direction, but with the same enzyme name. When processed in analysis it will produce two separate rows in the results table. PlasmidTools now adds a suffix '_L' to the enzyme name for the complementary recognition sequence in order to distinguish. This is required to position cut sites correctly when the project is reverse complemented. And naturally, if the non-palindromic recognition site is in the opposite direction, the 'enzyme_L' site will be to the right of the recognition sequence. (But always on the left side of the official forward-strand recognition sequence). When such enzymes are selected in the results table, the complementary listing is also selected automatically, and both are annotated when clicking the Annotate button.

1.2.2.1 (2016-01-17)
- Fixed some issues with displaying user-defined colours in the sequence pane when features were highlighted or the font was changed.

1.2.2.0 (2016-01-10)
- Added customization of the sequence pane colours, including text and background colours for sequence, annotations and feature highlighting. The colour chooser is opened in the Options menu (Options - Sequence pane colours).
- Fixed an issue in which hidden (inactive) project tabs not were locked/unlocked for editing when the results pane or annotation manager was opened/closed.

1.2.1.0 (2016-01-04)
User interface:
- Added customization of the text font used in the 'Sequence alignment editor'. The font may be set in the Options menu or in the alignment editor itself. If the computer does not have the default font (Courier New) installed, another monospace font may then be selected.
- Added some new functions in the Text editor.

1.2.0.18 (2015-12-12)
User interface:
- Added customization of the text fonts used in Sequence pane and Text editor. The fonts are set in the Options menu. Open sequence tabs and Text editor windows are updated instantly when changes are made.
Export:
- Fixed an issue with export to Genbank and EMBL formats in which the exported sequence was truncated if the exported sequence was less than 60 bp in length (less than one complete line).
- The numbering following the last line in EMBL export was incorrect.

1.2.0.17 (2015-11-22)
Sequence pane:
- Added two functions to generate reverse and complement sequence, respectively, of what is selected in the sequence pane. Any annotations contained inside the selection are ignored. The generated sequence, which in both cases is 3'-5', is displayed in a Text Editor window. The functions are useful for displaying minus strands and reverse primers in textual drawings, for example.
- Fixed a bug in the Cleanup function which crashed if the sequence had an annotation opening bracket (<) not followed by a closing bracket (>). Cleanup now ignores the sequences downstream of an unclosed opening bracket and displays a message about the issue, so that proper corrections can be made.

1.2.0.16 (2015-10-17)
Oligo primer analysis:
- The number of primers listed has been limited to max 200 in each direction. (By applying unconstrained criteria it was possible to have thousands of primers listed, which required lengthy processing and unresponsiveness).
Circular map:
- Added a function to the right-click menu for adjusting the relative size of the plasmid circle within the map area. By combining adjustments of window and circle size, more appropriate views can be made in situations with few or many annotations.

1.2.0.15 (2015-09-29)
Sequence alignment editor:
- The sequence numbering above the alignment did not adjust according to the sequence range set for the alignment.
- Some edits applied to the alignment did not mark the alignment as changed and did not raise the 'save-or-not' pop-up when closing a changed alignment.
Cloning tool:
- If a file-open operation was canceled, or could not be completed, any pre-existing file in the respective window was closed.

1.2.0.14 (2015-09-27)
Sequence alignment editor:
Added range parameters for the reference sequence. The range sets which part of the reference sequence is visible in the alignment and used by the aligning algorithm when aligning sequence reads. No need anymore to modify the reference sequence project file before opening it in the alignment to comply with the 3000 bp length limitation. Just open a sequence file of any length and set the range of interest.

1.2.0.13 (2015-09-22)
Service update (latest version of the restriction enzyme database; corrected some terms and wording in the Sequence Alignment Editor that could be confusing; changed the background highlight colour to something a bit more neutral.)

1.2.0.12 (2015-09-10)
Service update.
This update relates directly to the previous update, version 1.2.0.11. Please read it below before continuing.

While Windows XP cannot read the new SHA-2 (256-bit encrypted) digital certificates, later Windows versions do not like the old SHA-1, and pops up warning messages. To resolve it, two different PlasmidTools installation packages are now available, one for Windows XP (signed with SHA-1), and one for later Windows versions (signed with SHA-2).
Having two installers increase the chances that one might install the program over a pre-existing installed version. It's important to be aware of that running a full install may overwrite the custom sequence database. It's recommended to make backups of the database regularly by using the built-in export function. In case of  'disaster', the exported database can easily be restored through the built-in import function.

1.2.0.11 (2015-09-09)
Service update.
Became aware of that the digital certificate in the PlasmidTools installer (setup.exe) was not recognized on Windows XP systems. This has probably been the situation since January 2015, when the certificate was renewed, and automatically updated to the new SHA-2 (256-bit) security encryption. Windows XP is deprecated by Microsoft and does not receive updates, and therefore does not support todays encryption. As a result, Windows XP has been unable to read the certificate and would abort installation with an error message mentioning 'unknown publisher' and 'does not have a valid digital signature'. The certificate has now been downgraded to SHA-1 (128-bit) encryption, and I hope this will resolve the problem. Many large institutions still use XP (which is just tragic), so PlasmidTools will continue to support XP for a while.

1.2.0.10 (2015-09-07)
Project files opened using the recent-file list were marked as being changed when opened, causing the 'File changed' pop-up message to appear when closing an unmodified file.

1.2.0.9 (2015-09-06)
Cloning Tool:
The 'Ligate' function aborted if the plasmid selected as 'vector' was only linearized (cut by only one enzyme). I use the opportunity to remind users of PlasmidTools to report bugs to contact@plasmidtools.com.
General:
- Stopped an automatic removal of "_anynumber" from annotation text when files are opened. It was implemented to correct restriction-site annotations added by the earliest program versions, which added the text as a suffix. Later versions depend on the restriction-enzyme names being unmodified, to be able to lookup enzyme properties based on the text, which is needed to calculate cut position when switching strands (reverse complement).
- The program will from now on check for updates once a week, and after the program has started, to speed up start-up time. It also means that the message to apply a downloaded update will appear on the next run after the update was downloaded.

1.2.0.8 (2015-08-30)
Sequence pane:
- Extended the collection of keyboard buttons/characters that will cause immediate update of data structures and graphical maps if annotations are edited directly in the sequence pane.
- Also modified the 'Force map update' function, which was not as 'forceful' as intended, to force the update no matter what other pieces of code would think about it. Using the 'Force update maps' function is relevant if doing manual edits of annotations directly in the sequence pane and typing special characters and symbols that do not trigger automatic update of graphical maps.
Primer analysis:
Added the primer concentration as an adjustable parameter in the user interface.
General:
Removed the 'Old style' circular map.
Primer analysis update:
- Adjusted the default primer concentration from 50 to 200 nM (which is more common) and a primer-concentration parameter to better reflect the average conditions during amplification. The effect of the two adjustments combined is a ~1 degree celcius increase in Tm. (Primer and product concentrations, and Tm, changes during amplification. Fortunately, PCR and Sanger sequencing reactions are quite robust against Tm changes. Having a moderate 3' dG is more critical).
- Replaced the term Thyb with Tm throughout (since Thyb could mistakingly be interpreted as the hybridization temperature to use in PCR). Tm represents the temperature at which half of the sites to be primed are bound by primer.

1.2.0.6 (2015-08-19)
Primer analysis:
- Modified the check of adjustable parameters to allow positive cut-off values for primer-dimer dG. A message is presented if a value is set unusually stringent (since it is quite common to forget a minus sign now and then).
- The sequence pane now highlights forward and the reverse primers concurrently, using different colours for the two directions.
- Automatic highlighting of selected primers in the sequence pane 'froze' after running 'Find primers', and needed a selection change before continuing.
Sequence pane:
- Changed the sequence-pane highlighting colour for better contrast and clarity.

1.2.0.5 (2015-08-11)
Primer analysis:
- The default primer search ranges set when starting Primer analysis, being the first and last 100 bp, did not adjust properly if the project sequence to analyse was less than 100 bp in length.

1.2.0.4 (2015-08-08)
Primer analysis:
- Primers shorter than 'Maximum primer length' could not be mapped in the very start of the search range, but was limited to having a 3' end at 'Maximum primer length' position or greater.
- The last nucleotide in search range was not included in analysis.
- 'Primer report' now lists the parameters used to calculate dG and Tm values.
Linear map:
- Fixed an issue in which the position of point-annotation labels (cut sites etc.) in certain situations could be set too low and overlap other labels. The fixed algorithm also works faster.

1.2.0.3 (2015-08-02)
Primer analysis:
- Fixed an issue with the default pre-entered values for Na+/K+/Mg2+/dNTP concentrations, which were not recognized as legitimate decimal numbers on systems using comma (',') as decimal separator.

1.2.0.2 (2015-08-01)
Primer analysis:
- Added textual drawings of primer-dimer interactions in 'Primer report' .

1.2.0.1 (2015-07-23)
Primer analysis:
- Fixed an issue that caused a warning message if 'Annotate' or right-click menu items were clicked when one or both primer tables were empty. 'Annotate' and 'Primer report' now processes what is selected in one or both tables.

1.2.0.0 (2015-07-22)
Added oligo primer analysis for designing PCR and sequencing primers.

1.1.9.2 (2015-04-06)
Service update (some small fixes and additions and improved graphics).

1.1.9.1 (2015-03-31)
Service update (might have been a problem when running the enzyme filter for the first time after upgrade, depending on OS version).

1.1.9.0 (2015-03-28)
User interface:
- Layout rearrangement, smaller buttons, and some moved to more appropriate locations.
- Overflow function in button panels to cope with limited-space problems on small monitors in a better way.
Cloning Tool:
- The function crashed if the 'Ligate' button was clicked before having two sequences open.
Service update (ensure use of monospace font (Courier New) in file export etc.).

1.1.8.0 (2015-02-02)
File import:
- Rewrite of the import function used when importing files and adding files in the Sequence Alignment editor. The new import function auto-detects the sequence format based on file content. This facilitates import of non-standard file types like *.seq, which may have different internal formats, and simplifies import in general. See the Manual for details.
- Fixed a bug in the import of GenBank files, which crashed if the file had a CDS annotation in reverse direction.
System:
- Prevented duplicate opening of windows and functions that could cause conflicts, including  items on the Options menu and the 'Sequence Db' and 'Cloning Tool' functions, which are able to change program settings.

1.1.7.13 (2015-01-22)
Sequence alignment:
- Program crashed if 'Right-click-Gap in others' was clicked in an empty alignment.
- When an unsaved alignment was closed due to opening a new one, the closing alignment was not saved although this was the selected choice.
- The window heading showing the name of the alignment file was not reset when alignment was closed.

1.1.7.12 (2015-01-19)
System:
- The PlasmidTools file types (.ptools, .seqdb, .ptalign) should now register correctly in most Windows versions during installation. Due to the backwards compatibility implemented (XP SP3), there may be issues in the latest versions (8, 8.1). In case of problems, right-click a PlasmidTools file and select 'Open in..' and select PlasmidTools and to always open in this program.
- When double-clicking a PlasmidTools project file (.ptools) in Windows File Explorer, the file will now open up in PlasmidTools. It's a requirement that the PlasmidTools file types are properly registered in Windows (see above). The clicked file will open up in a new PlasmidTools window, regardless of pre-existing running instances. It will set the active directory so that any file-open operation will default to the same folder.

1.1.7.4-11 (2015-01-19)
Service updates. Working to sort out file associations and opening of files double-clicked in file explorer (this cannot be done in the software-development environment).

1.1.7.3 (2015-01-11)
Sequence alignment editor:
- Added a new function to the right-click menu: 'Realign all'. The function performs a realign of all sequence reads with the reference sequence present in the alignment view. Particularly useful when replacing the reference with a new sequence.
- Prevented the insertion of linebreaks in the sequence-name list.
- Fixed a problem in the 'Realign' function. Program could crash if the function was executed directly after opening a saved alignment file and no sequences had been added in the session.

1.1.7.2 (2015-01-07)
Sequence alignment editor:
- The forward(+)/reverse(-) indicator in front of the sequence name was constitutively changed to (+) after a realign.
- Adding of sequence read that has no continous match is now added to the alignment unaligned. It's up to the user what to do with it.

1.1.7.1 (2014-12-28)
Service update.

1.1.7.0 (2014-12-14)
Added a sequence alignment editor designed to handle sequencing projects. Sequences reads will be checked against both strands of a reference sequence and aligned in correct position and orientation. The alignment can be further edited as wished, colour coding is updated automatically. The function is launched from the analysis menu. A lot more to say about the alignment editor, see the online manual for more information.

1.1.6.1 (2014-11-23)
Service update (added continuous updating of the position label when cursor position is changed by use of arrow keys etc., and some small fixes).

1.1.6.0 (2014-11-16)
Rewrite of basic algorithms resulting in better responsiveness in general, and greatly reduces processing times in many situations. For example, loading and processing of a 30.000 long project sequence with hundreds of annotations now takes 1/75 of the time in previous versions (on my laptop: 2 seconds, compared to 150 seconds in earlier versions).

1.1.5.1 (2014-11-13)
- Fixed stability issues connected to manual editing of annotations and brackets in the sequence tab editor.
- Optimization of lower-level algorithms to make most things go faster.

1.1.5.0 (2014-11-07)
Sequence editor:
- The automatic insertion of annotation brackets (<>) when pushing the '<' button may not work with all country-specific keyboard layouts. Previous version (1.1.4) should handle Scandinavian keyboards, at least, and this latest version also English keyboard layout. If you experience problems with this function, please send a message to contact@plasmidtools.com with information about country and position of the '<' button on the keyboard.
- Added a new menu item to the sequence tab right-click menu for inserting a pair of annotation brackets (<>) in the sequence. Insertion is done at cursor position. This is the recommended method for adding annotations when doing manual editing since it is independent of region settings and keyboard layout.
File export:
- Fixed a bug in the 'Export project to GenBank format' function in which the process could abort if the last line of sequence to be written had less than 10 residues.

1.1.4.0 (2014-11-04)
Sequence editor:
- Fixed a problem in the monitoring of manual edits in the sequence editor and subsequent updating of graphical maps. The maps and 'behind-the-scenes' data structures now updates instantly on any relevant edit done in the sequence editor.
- When, or if, inserting annotations in the sequence editor manually, a single push on the angle-bracket button now inserts both starting and ending brackets side by side (to ensure stable program execution). It is advisable to fill in the annotation text directly.

1.1.3.3 (2014-10-31)
Service update. (Various improvements in windows logic when switching sequence tabs and changing sequence properties; removed automatic word selection in editors).

1.1.3.2 (2014-10-20)
Service update.

1.1.3.1 (2014-10-19)
Service update.

1.1.3.0 (2014-10-17)
System:
- Added Cut/Copy/Paste menu items to the right-click menus in the project sequence tabs and text editor windows. The keyboard alternatives are of course still available.
- Added a function to copy the linear and circular maps to the windows clipboard. The graphics format is Windows bitmap and can be pasted in most documents and programs, incl. Microsoft Office. 'Copy to clipboard' is found on the right-click menus.
- Added a list of recently used files to the File menu. Project files opened or saved as new file will be put on top of the list.
Text editor:
- Fixed a problem in the Text Editor in which clicking the save button could crash the program. This happened in the special situation when the text editor was launched by the project export function, and the project was a new unsaved project with no associated filename.

1.1.2.1 (2014-10-14)
Service update.

1.1.2.0 (2014-10-12)
System:
- Added separate colour choosers for the linear and circular maps, since the requirements are different.
- New constructs generated with the Cloning Tool now open up in new project tabs in the main window (instead of being saved directly to disk as in earlier versions).
- The system with automatic enabling/disabling of menu items and buttons has been discontinued. Instead of showing a lot of greyed-out buttons and elements without any explanation why, all menu items and buttons are now enabled at all times, and if clicking an item that has no meaning in a specific situation, a message is presented describing its function and requirements. To experienced users of PlasmidTools it makes no practical difference,  but new users may find it helpful and clarifying.

1.1.1.2 (2014-10-02)
Service update.

1.1.1.1 (2014-09-23)
Fixed an issue with the colour chooser not working if no project was open.

1.1.1.x (2014-09-22)
System:
- Added a colour chooser for the graphical map to enable customised colours on the different types of graphical elements. The colour chooser is launched from the Options menu.
- Fixed an issue where the first sequence opened (left-most tab) had a 'frozen' sequence name not reflecting changes made to the sequence-name field.

1.1.0.3 (2014-09-19)
Cloning tool:
- The Cloning Tool displayed a runtime error if trying to open a sequence not being DNA, or clicking the Ligate button before having two sequences open.
System:
- The sequence-tab labels did not update when editing the sequence-name field.
- Adjustments to the linear map (grey lines around regions for better clarity; more space above the centre line).

1.1.0.2 (2014-09-14)
Service update with adjustments in the multiple-document interface:
- Prevent duplicate opening of the same file.
- Distinguish opened files independently of project features like sequence name, which means that any collection of files may be handled side by side as long as they represent different files on disk.
- Other adjustments in windows logic when switching active project.

1.1.0.1 (2014-09-07)
- Update of the Restore point/Undo and Import functions to fit with the new multiple-document interface.
- Some adjustments to how result panes and windows respond when switching active project.

1.1.0.x (2014-09-02)
Program has been upgraded with a Multi Document Interface (MDI). An unlimited number of project files (sequences) may be worked on side by side in a tab-based arrangement.

1.0.15.1 (2014-08-26)
Added more species-specific codon usage tables for analysis of coding sequence.

1.0.15.x (2014-08-20)
- Overhaul of the Circular map view to make it more compact and safe against overlaid text and elements. Overlapping ORFs and regions are now shifted inwards in the circle, and labelling of dispersed and grouped features is more uniform and better organized. The old strategy, in which closely positioned features were grouped and labelled further out from the centre, is still available on the main menu (Options – Circular map (old style)), although it has been improved somewhat by inwards shifting of regions.
- Added a new main menu item, Resources. It provides access to data used in analysis. To begin with, it has the codon usage tables for the species available in analysis.
- Fixed a bug in the Cloning Tool in which changing the enzyme filtering options did not cause the enzymes list to update to the new settings.

1.0.14.x (2014-08-16)
Added a new function related to codon usage quality. The function will analyse a given open reading frame and output a list of species-specific codon usage statistics for each codon triplet through the sequence. The function is available on the Analysis and right-click menus. In this first version, codon/translation quality may be analysed in Homo sapiens, Mus musculus, Saccharomyces cerevisia and Escherichia coli. More will come.

1.0.13.x (2014-07-31)
- Fixed a bug in the translation to protein function in which A residues became duplicated in the output file. The bug was probably introduced in the recent version 1.0.10.x when the translation function was reorganized. Please check protein sequences made with the latest program versions for duplicated A's, or redo the translations to ensure the sequences are correct.
- Overhaul of the translation to protein function resulting in faster processing.

1.0.12.x (2014-06-15)
- Added circular map view. The map can be opened from the Options menu and from the linear map right-click menu. The circular map is displayed in a separate window and is updated automatically along with the linear map.
- When running the 'Simulate digest' function, any selected Gateway recombination sites are now excluded from analysis.
- Newly added Gateway sites should now automatically appear in the 'enzymes' list after applying a program update (no need to click the 'save changes' button in the enzyme filtering options).

1.0.11.x (2014-05-25)
- Added right-click menus to the results panes. Mostly short-cuts, but also some extra functionality.
- Added more Gateway recombination-site variants.

1.0.10.x (2014-05-19)
- 'Translation to protein' function moved to the Analysis menu, and is no longer done by changing the sequence type to 'Protein'. As in previous versions, translation starts from the current cursor position, in forward direction, and ends on the first in-frame stop codon reached. The resulting protein sequence opens up in a text editor window and can be saved to file or copied to a project or document. The open DNA/RNA project is not changed.
- Search function modified to handle sequences crossing the zero position in a circular sequence.

1.0.9.x (2014-05-13)
Cloning Tool:
- Added the possibility to adjust enzyme filtering options inside the Cloning Tool.
- Gateway cloning has been restricted to allow legal operations only: B sites can be recombined with P sites, L sites with R sites.
- Fixed an issue where certain compatible ends were not recognised as such. The problem affected the special situation where a non-palindromic site was mapped on the reverse strand and the associated fragment then turned around to check for complementarity to another end.
- Added more Gateway site variants (applicable to sequence Db scan, Restriction site analysis and Cloning Tool).
System:
- Fixed an issue introduced in version 1.0.7 in which non-capital letters were overlooked in restriction site mapping (major slip after a lot of code rewriting, I'm sorry).

1.0.8.x (2014-04-23)
- Fixed a start-up problem related to the new restriction enzyme filtering options after updating to ver. 1.0.7. An error message was shown referring to 'UsedEnzymes'. This would not happen after a fresh install. The problem can be fixed in ver. 1.0.7 by going to the 'Restriction enzyme filter' in the Options menu and click the 'Save changes' button. The best option, however, is to apply this latest update which offer additional improvements.
- Fixed an issue in the Cloning Tool where Gateway recombination sites, if selected in the 'Restriction enzyme filter', would not map correctly, or not at all. The Cloning Tool was not originally designed to deal with Gateway sites. However, with the optional inclusion of Gateway sites via the enzyme filter, the solution was to have Gateway cloning implemented. When using the Cloning Tool to simulate Gateway recombination cloning, the user must take responsibility for following the Gateway rules: B-sites react only with P-sites, L-sites react only with R-sites. The program takes care of distinguishing left sites (X1) from right sites (X2).

1.0.7.x (2014-04-22)
Restriction enzyme analysis:
- Added more options to filter which enzymes are included in analysis. Filtering options are available from the main menu: Options - Restriction enzyme filter. By default, rarely used enzymes are excluded from analysis.
- Added Gateway recombination sites as a group of 'restriction enzymes'. To include Gateway sites in analysis it must be activated in the enzyme filtering options. Annotating of a Gateway site through restriction enzyme analysis will produce a point annotation at the start of the core sequence, analogous to restriction enzyme overhangs.
- Optimization of the enzyme scan engine resulting in considerable speed gain.
- Fixed an issue where positioning of an ambiguous restriction enzyme cut site matched on the minus strand was set according to the minus strand cut position. Now it will show the plus strand cut position.
Sequence database:
- Added two built-in databases: Gateway recombination sites, and antibiotic resistance genes. These are not customizable. To include these databases when scanning project files, select the corresponding categories in the Sequence Db scan filter available from the Options menu. Annotating of Gateway sites through Sequence Db scanning will produce a region annotation of the directional type (arrow) covering a unique 25-bp footprint surrounding the recombination core sequence.The customizable user database is kept separate from the built-in databases and can be modified, exported and imported as in previous versions.
Cloning Tool:
- When making a new construct by clicking the Ligate button the user will be presented an overview of the new construct before deciding to save or not.

1.0.6.x (2014-03-24)
Sequence database scan function:
- Scanning of project sequence for matching items would not detect features spanning the zero position in a circular sequence.
- The offset value was neglected when positioning a point annotation.
Cloning Tool:
- The columns showing name of enzyme cutting at the 5' and 3' ends now display actual name also for blunt cutters, not 'Blunt' as in previous versions.
- Added additional information about the opened files.

1.0.5.x (2014-03-19)
Highlighting of features in the sequence pane:
- Highlighting of cut site in position 0 caused runtime error.
- Highlighting of region spanning position 0 would not show.
- Highlight colour on features could spread to the entire sequence.

1.0.4.x (2014-03-17)
Added a new function called 'Cloning Tool'. The Cloning Tool will generate new constructs with minimal user interaction. Open the Cloning Tool, select two sequences and enzymes for digestion, select from generated fragments, and click a button to make and save a new construct.

1.0.3.x (2014-02-25)
The PlasmidTools installer is from this on secured with a digital certificate from DigiCert to ensure its authenticity during download and installation. If the installer has been altered or tampered with after its release, the certificate will be invalidated and the user will get a specific warning about this when starting installation.

1.0.2.x (2014-02-14)
Fixed an issue when opening a PlasmidTools project file by double-clicking it in Windows Explorer, PlasmidTools would start, but not open the clicked file.

1.0.1.x (2014-02-07)
Fixed a problem where the program could crash or display an error message (null-reference) when closing or clicking on certain areas in the 'Manage annotations' pane.

1.0.0.x  (2014-02-04)
First public release.