SimPlot Features

SimPlot Features

Features labeled New have been added since version 2.5. This list is not meant to be exhaustive. See Version History for chronological (and more complete) list

Sequence management interface
Autodetection of a variety of file formats
o From Don Gilbert's ReadSeq code: CLUSTAL, EMBL, Fasta/Pearson, Fitch, GCG/Wisconsin, GenBank, IG/Stanford, NBRF, Strider, Zuker
o Added: GDE flat file(New), MASE, MSF(New), Nexus/PAUP(New), PHYLIP (interleaved and sequential)
Sequence names can be long, and contain punctuation characters
Hierarchical display of groups
o Groups can be created, deleted, renamed manually
o Groups can be autodected based on the first character(s) of sequence names, or (New) the character(s) prior to the Nth occurrence of a character separator (e.g. "_")
o Sequences can be moved among groups by mouse-dragging or using buttons
New Groups and sequences can be individually de-selected (allowing use of a large "master" alignment)
New Unlimited (except by available memory) number of groups
New Colors can be assigned on SeqPage, and assignments are used in subsequent analyses
o Unlimited (except by available memory) number of sequences in each group
NewSave groups - saves currently-displayed groups (and colors) in Nexus (PAUP*) format, eliminating need to re-create groupings each time
Export "slice" of alignment
o User selects start/stop positions
o Output file format selectable from Save dialog (list of choices above)

Interactive Similarity/Distance plots
Visualize how related one sequence is to a panel of other sequences or groups of sequences
NewSave output as comma-delimited text (*.csv). Can be opened directly in Excel and other programs for customized figures
Options:
o Jukes-Cantor, Kimura, and F84("Maximum Likelihood") corrections for superimposed substitutions
o Plot of distance or similarity, 0-100 or 0-1 scale
o Selectable reference type for comparison to sequence group - consensus sequence or average distance
o Transition/transversion ratio selectable by user, or can be estimated empirically either for the entire alignment or for each window (New)

Bootscanning
NewNo longer requires installation of PHYLIP programs
NewBootscan values are saved, so that user can click on any series in legend and view bootscan result using that series as query
NewAt end of bootscan user can be notified of evidence of recombination, indicating putative recombinant (i.e. recombination in non-query sequence can be detected)
NewSupport for external PHYLIP programs updated to current version (v3.6a2.1 as of this writing). NOT compatible with older versions due to changes in PHYLIP menus in version 3.6
Bootscan-specific options include (see below for other options):
o Number of bootstrap replicates (50-1000)
o Tree construction model: Neighbor-joining (NEIGHBOR) or Maximum Likelihood (DNAML)
Support for DNA Parsimony (DNAPARS) and Fitch-Margoliash (FITCH) removed - please notify author if you need these
o Transition/transversion ratio
o For distance methods: Kimura (2-parameter) versus Maximum-likelihood
o Save CONSENSE output for later viewing (see comments on this)
Fast: on a 550 MHz laptop, a full-length HIV-1 bootscan (37 sequences in 8 subtypes, plus the query sequence) with a window size of 500 and a step size of 20 (about 400 windows, 100 permuted Neighbor-Joining trees in each window = 40,000 trees) with Kimura (2-parameter) correction takes less than 10 minutes (your mileage may vary - actually, your computer is probably faster than mine!)
Faster: on a 1.3 GHz laptop,a full-length HIV-1 bootscan (58 sequences in 8 subtypes, plus the query sequence) with a window size of 500 and a step size of 20 (more than 350 windows, 100 permuted Neighbor-Joining trees in each window = >35,000 trees) with HKY85 (2-parameter plus gamma-distributed rates) correction takes less than 5 minutes (your mileage may vary - actually, your computer is probably faster than mine!)
NewBootscanning functions under Windows NT, 2000, and XP

Options and features that apply to both types of plots:
NewSupport for Interpolated plots - positions along the alignment are analyzed in non-sequential order, rapidly giving an indication of the results
NewSupport for PAUP* in Similarity/Distance plots and bootscanning
NewInteractive analysis for breakpoint location using informative sites (see Getting Started for an example)
NewSum of Chi-squared values displayed on chart
NewUser-controlled position of informative sites results on chart
NewIndividual sequences, or groups of sequences, can be used
NewWhen groups are used, stringency of site conservation is selectable
NewAutomated inference of breakpoints through maximization of chi-squared
NewDisplay of breakpoints as "fuzzy", with bars to indicate interval of equivalency
Any sequence (or group) can be the query sequence
Save/Copy plot as bitmap or metafile (metafile can be manipulated in presentation programs like Microsoft PowerPoint)
NewSave plot data in comma-delimited (*.csv) format, which can be opened directly in Excel and many other programs for customized plotting
Gap stripping (ignore sites containing gaps)
Gap threshold (what % of sites in a window need to be non-gaps for the value to be plotted?)
Window size, step size for sliding window
NewUser-defined window and step sizes, in addition to preset values
NewChart editor, for detailed control over display of charts, including previously available options:
User-definable vertical axis range, including (New)Auto-scale axis to accomodate existing values
Consensus threshold (when applicable)
Plot as line (varying thickness) or points (varying size) or both
Include any (or none) of the following in the plot
o Title
o Source file name
o Symbol legend
o Parameter settings
o X and/or Y grid lines
Zoom in/out (just draw a box from top-left to bottom-right of area to be viewed)
Panning while zoomed in (right-click and drag)
Left-Click on any point to identify sequence, position, and Y-axis value
Right-Click on any curve to change its color

FindSites: Automated identification of informative sites for the next step in analysis of mosaicism (see Background)
This refers to the feature as implemented on the FindSites page. More detailed information than Interactive version noted above.

QuickTree and QuickBootstrap
NewWhen two marks are selected, these options are available from the Commands menu. The current phylogenetic settings are used to generate a tree is generated.

Save options/restore default settings

Recently-opened file list