Simmap News

21 July 2010 -- v1.5.2 Build 21072010 is released to address a minor output bug in saving mutational history trees.

  1. A minor bug was fixed in which the branch lengths (not the mutational lengths) in saved trees was not rescaled by the rate multiplier. This bug did not effect correlation analyses, codon analyses, positive selection, or any of the collected statistics. If the individual statistics for each mutational realization were saved then the branch lengths can be rescaled using the rate multiplier for each realization.

26 Feb 2010 -- v1.5.1 Build 26022010.1 is released to address a SERIOUS, CRITICAL BUG in morphological/standard analyses.

  1. A SERIOUS CRITICAL bug in rescaling the Q matrix such that the expected number of substitutions is 1. The bug has been fixed. This bug affected morphological/standard analyses only. The analyses affected where: standard mutational maps, character correlation, and ancestral states. The affect of the bug seems to be to marginally underestimate the uncertainty in ancestral states leading to overconfidence in an ASR analysis and underestimates in the number of substitutions in mutational mapping. PLEASE VERIFY THE CONCLUSIONS OF ALL ANALYSES.

19 Feb 2010 -- Build 19022010 is released.

  1. A new feature for selecting parameters of the prior distributions. Briefly, the approach uses MCMC to determine the posterior distribution of overall rates and bias values (two-state models) and then MLE to find the best fit Gamma and Beta distributions. The last phase uses the R statistical package and a R script I wrote. For an example, see the contents of the Priors folder in the distribution and the Help Documentation.

25 Jan 2010 -- Build 25012010 is released. The following fixes/changes have been made in this build:

  1. Fixed a bug reported (by a user) in which an analysis of positive selection would crash when the number of trees and parameters were not equal and the Link parameters option was active.
  2. Added additional options to the Help menu. You still need an active internet link to access these new options.

13 Dec 2009 -- Online website documents completed

  1. I have finished the online documents. I will make minor changes in the future, but all of the necessary information is now available.

10 Dec 2009 -- New build available, Build 10122009

  1. The Help menu item is now active. The help menu item will open the Help documents on the programs website in your default web browser.

09 Dec 2009 -- Made a few changes to the website:

  1. The website now points exclusively to the version 1.5 site. The version 1.0 has been deprecated. However, you can still visit the site here.

02 Dec 2009 -- Build 02122009.1 is released. The following fixes/changes have been made in this build:

  1. Fixed a bug in which the dwell times for morphological/standard characters was incorrectly reported in the summary statistics.
  2. Optimised memory usage between analyses. The behaviour now is that only the most recent analysis results are stored in memory. All previous analyses, regardless of the type of analysis, are released.
  3. Changed how significance is reported in the correlation results window. Overall statistics p-values that are less than 0.05 are shown in red. Individual statistics p-values that are less than 0.025 are shown in red. Testing significance in the individual statistic case is a two-sided test.

02 Dec 2009 -- Build 02122009 is released. The following fixes/changes have been made in this build:

  1. Problem in which trees without branch lengths can go unnoticed and cause a crash when an analysis or mutational map is requested. This fix will warn the user and then apply fixed branch lengths to all the trees. Alternatively, the user can cancel the file load.
  2. Problem in which a root branch length exists. This has been fixed and the length is now successfully ignored.
  3. Fixed a bug which caused an error in reporting morphological/standard dwell times.

20 Nov 2009 -- Build 19112009 is released. The following fixes/changes have been made in this build:

  1. Optimised memory usage when performing an ASR analysis. This alleviates problems when analysing very large data sets.
  2. Changed how ASR results are reported. See the ReadMe.rtf in the software distribution or the Documentation for more details.

10 Nov 2009 -- Build 10112009 is released. All of the features have been implemented and are currently being tested. The following fixes/changes have been to this build:

  1. Estimating positive selection has been implemented.
  2. Fixed the problem in which changes to the data matrix are not immediately reflected in the Tree View.

07 Nov 2009 -- Build 07112009.0 is released with the following fixes/changes:

  1. Mutational mapping of codons and collecting codon/amino acid residue statistics has been implemented.

19 Oct 2009 -- Build 19102009.2 is released with the following fixes/changes:

  1. When saving predictive statistics the values written to the file are the posterior predictive expectations. These are the values used to calculate the posterior predictive p-value. If you wish for each individual replicate you will need to save the predictive maps for each replicate and analyze them independently.

19 Oct 2009 -- Build 19102009.1 is released with the following fixes/changes:

  1. Fixed problem in reporting p-values associated with character correlations. P-values were not being properly evaluated for zero equality. All previous analyses should be redone and confirmed.

19 Oct 2009 -- Build 19102009 is released with the following fixes/changes:

  1. Fixed a problem with the rooting window that prevented the full taxon labels to be seen.
  2. Fixed memory leaks in the character correlation analysis that potentially led to a crash.
  3. Fixed problems with the progress indicator not reflecting the true progress of an analysis.
  4. Completed the code for nucleotide character correlation analysis. Now all possible uses of parameters and trees are available.
  5. Fixed a problem in the predictive analysis of character correlations which failed to account for equality between the observed statistic and the predictive statistic.

20 Aug 2009 -- Build 20082009 is released with the following fixes/changes:

  1. Fixed a number of window resizing issues.
  2. Moved the singleton and codon switches to the Characters box in the General Tab of the Analysis window.
  3. Added keyboard shortcuts to open the Models window (cmd-1) and the Analysis window (cmd-2).
  4. Implemented a class supporting different genetic codes.

13 Aug 2009 -- Build 14082009 is released with the following fixes/changes:

  1. The summary statistics from a standard mutational analysis appearing in the "Summary Statistics" window can now be saved to a file.
  2. The summary results from a correlated character analysis appearing in the "Correlated Character Statistics" window can now be saved to a file.
  3. The results from an ancestral states analysis appearing in the "Ancestral States" window can now be saved to a file.
  4. Trees exported in Phylip format now use the taxon label rather than the translate block numerical identifier.
  5. A program (Nex2Xml) is now available in the distribution for converting Nexus and parameter files to the Xml format used by SIMMAP 1.5.

12 Aug 2009 -- A file conversion utility for generating the required Xml file is released.

03 Mar 2009 -- Build 04032009 is released.

03 Mar 2009 -- New website is opened.