Version history

Version history

See SimPlot Features for listing of features by subject.

version 3.5 - August 15, 2003
Bootscanning under Windows XP no longer generates frequent error messages
Display of Regions
Fixed bug in saving raw chart values to text
Handling of colors moved to SeqPage
Large number of colors can be saved with Preferences and re-used
Groups identification by characters prior to the Nth occurrence of a separator (e.g. '_'), rather than a certain number of characters in a sequence name

version 3.4 - June 7, 2003
Enhancements of Findsites using groups:
Selectable threshold for degree of conservation (Options menu)
Added Histogram page, which displays a histogram of distances from similarity/distance plot when Hamming distance is used
Added support for MSF files and GDE flat files
Empirical determination of Ts/Tv ratio enabled
Added option to determine empirical Ts/Tv ratio for each window
Added QuickBootstrap command to Commands window (visible when 2 marks are selected). QuickTree has been available for a few versions
Fixes:
Vertical axis for similarity plots now labeled "Similarity Score", and "%" removed since these values are percentages only for Hamming distance
Error due to inclusion of "~" as a gap character now trapped
Locales that use characters other than "." as a decimal separator now supported during bootscanning
Changes to Ts/Tv ratio now properly registered when user clicks "OK" (thanks to Steve Oberste for providing details to stamp this one out)
Sequence names that begin with "_" no longer generate a "range check error" when only the first character is being used to identify groups

version 3.2 - March 30, 2002
FindSites enhancements/fixes:
Sum of ChiSqr now displayed on right side of plot (if zoomed, only visible values are summed)
User can now reposition FindSites results on chart using up/down arrows next to FindSites checkbox above charts
FindSites data now labeled with Sequence or Group name
At end of bootscan, [optional] prompt indicating evidence of recombination now provides the name(s) of the potentially recombinant group(s)
Options menu cleaned up - most analytical options moved to Preferences submenu (PlotOptionsU)
FirstPosition is now stored as a user preference
Query series now inactive (hidden) in bootscan, with proper handling when user clicks on another series in legend, thereby selecting a new query series
Similarity/Difference plot vertical axis changes now result in immediate recalculation of existing data
During analysis, switching pages now prevented. This avoids some of the errors that were caused by switching to the SeqPage during a plot; switching to SeqPage resets the Query group, so on switching back to a plot the (ongoing calculations were referencing a nonexistent query)
Bug fixes (cosmetic):
When zoomed and panning, ChiSqr value of -99 was shown along Y axis when a mark had scrolled out of view to the left
Buttons for moving marks did not always work in SimPlot

version 3.13 - March 25, 2002
Restored support for external PHYLIP programs
Bug fixes:
Bootscanning generated an error when a group had been de-selected in the middle of the list
SeqPage drag-and-drop now works

version 3.05 - February 18, 2002
Added export of raw data from chart to CSV
Added "Other..." Window size and Step size (allow user-defined sizes)
Recompiled under Delphi6, fixed numerous small bugs, further encapsulated TSqListGrp object
Removed ErrCode from TSqAlignment.ReadSeq
Added "Win2000" to name, removed "Win95" to reflect test systems
Added ability to include ambiguous characters in sequences calculated for FindSites, Consensus
Added option to save settings as defaults in PlotOptionsU
Cursor changed to crAppStart (rather than hourglass) to reflect user's ability to do other things while a task is running
Start and Stop buttons for SimPlot and BootScan now separate controls, so that user can start and stop them independently (internally, booleans also made independent).
Bug fixes (minor interface glitches)

version 3.0 - March, 2001
Added SaveGroups (Nexus format, including "RaySoft" block)
Added Interactive FindSites
BootScan stores data for all query groups, displays one, user can click on others in legend to see the plot
Bootscan allows "detection" of recombination events, based on a threshold for bootscan values for identification of a parental sequence. If more than one parental is identified for any sequence, it triggers (optional) notification of a potential recombination event.
Clicking on another group in the Simplot legend changes Query to that group, and runs SimPlot
When SimPlot or Bootscan requested, and there are >= 2 marks, user is prompted whether to limit scan to region between first 2 marks.
Interface for FindSites changed to ComboBoxes on SeqPage

version 2.8 - March, 2000
User is alerted when sequences share the same name, though sequences are loaded anyway
Sequence names can now be arbitrarily long. User is alerted if file name will be truncated, e.g. when saving in PHYLIP format from SaveSlice...
Changed SqGrp to a dynamic array of TSqGrp, which was moved to TSqGrpU (to be shared with VarPlot)
Enhanced Markers (introduced in version 2.6), which allow focused analysis
Set/cleared by double-clicking the plot background
Moved by either clicking near a mark, or using the arrows which appear just above the plot area (allowing exact placement)
When at least 2 markers are set, Plots are focused to the segment bounded by the 2 leftmost marks
When exactly two markers are set, the following functions are enabled:
Quick Tree under the Command menu creates a tree using the current Distance Model and Tree Model settings, and launches the tree file (works well with Rod Page's excellent TreeView program)
Save Slice of Alignment... (under File menu) uses the marked interval
Changed TDistModel (see v2.6) to an enumerated type defined in MyReadSq, which is more strongly typed and standardized across multiple applications.

version 2.7 - November 7, 1999
Added PHYLIP DNADIST code as a module, modified to use memory rather than disk storage of input and output, GREATLY speeding SPlotPage. Need to adapt for use by Bootscanning, as DNADIST is the slowest step.

version 2.6 - March 25, 1999
Added Kimura and MaxLikelihood models to SPlotPage (they are slow!)
PROTDIST and PROTPARS to BootScan
Marks added to control region of analysis
Fixed GetPhylipDir bug (user unable to select directory)
Changed TDistModel to be an integer mapping integer constants to a string array

version 2.5 - March 18, 1999
Uses Windows 95 (32-bit) version of PHYLIP for bootscanning
Bootscan now works under Windows NT (as well as Windows 95/98)
Fixed bug in SeqPage code that allowed nesting of groups

version 2.4 - March 4, 1999
Bootscan arbitrary number of groups
Optionally save CONSENSE output files for later viewing
View PHYLIP Directory menu item (under Files) available from BootScan page to view these CONSENSE files or just check on location and files present
Help menu item added to send email to author
Fixed AutoUpdate menu item status, which was not initialized on launch
Resizing of sequence page now retains appearance
Handling of '*' and 'N' characters - now ignored (mostly an issue with files from Los Alamos site)

version 2.31 - February 26, 1999
Removed the OutGroup selection for Bootscanning - not really relevant.
Restored the Print menu item under File (omission from v2.3)
PHYLIP programs can be located anywhere on disk!

version 2.3 - February 22, 1999
New sequence selection interface
Arbitrary alphanumeric sequence names allowed (excluding spaces)
Plots are no longer erased when switching panes
Additional bootscan tree algorithms - FITCH, DNAPARS
Save Slice... allows selection of file format

versions 2.22-2.24 - minor bug fixes

version 2.21 - February 10, 1999
Fixed bootscanning bugs causing crashes, notably switched from a ShellExecute call to CreateProcess.

version 2.2 - February 6, 1999
Bootscanning added!
Multi-panel interface

version 2.1 - January 21, 1999
Added ReOpen menu
Fixed bug causing 'out of memory' error (related to file name truncation)

version 2.0 - January 3, 1999 (thanks to Mika Salminen for suggesting many of these changes)
Comparison of query sequence to Groups of sequences
Comparison to 26 individual sequences or groups of sequences (limit was 10 sequences in version 1.x)
Unlimited (except by available memory) number of sequences in each group
Jukes-Cantor correction for superimposed substitutions
Choice of plot type: distance or similarity
User-definable vertical axis range
Selectable reference type for comparison to sequence group - consensus sequence or average distance
On-the-fly consensus sequence determination
Save options/restore default settings
Right-Click on any curve to change its color

version 1.4beta - August 6, 1998 (never fully released)
Export of plots as enhanced Windows metafiles, allowing manipulation in graphics programs like Microsoft PowerPoint
Export of "slice" of alignment for phylogenetic testing of mosaicism

version 1.3 - July 31, 1998
Added autodetection of file formats, using ReadSeq code from DonGilbert at Indiana University
Added selection of sequences from an arbitrarily large alignment
Fixed bug which prevented recognition of informative sites if sequences were in lowercase

version 1.2.2 - May 19, 1998
Removed bevel from edge of chart (looked bad after copy & paste)

version 1.2.1 - May 18, 1998
Fixed problem with fasta file reading detected by Carla Kuiken at the HIV Database and Analysis Group, Los Alamos National Laboratory - thank you!

version 1.2 - May 11, 1998
Added Bitmap file save
Added demo file ("Gag_Demo.fsa", which includes 93BR029, a Brazilian gag sequence known to be a mosaic of subtypes B an F)
Fixed printing bug
Fixed annoying error that occurred when user clicked the axes

version 1.1 - April 26, 1998 - First public version