20 February 2009

Build 20022009-1.0-2.4 released. This build fixes a bug cuasing a full program crash when reading tree files out by BEAST.

3 August 2008

Build 03082008-1.0-2.4 released. This build fixes a number of bugs and introduces a new feature. The molecular model selected for the analysis can be viewed by using the "Show Model" option in the "Models" main menu item. In addition, the output of ancestral states has been changed to enhance its display and make it easier to import into a program for further analysis and preparation for publication.

31 July 2007

Build 29072007-1.0-2.3.2 released. This build updates the built in Help documents and extends the fix ancestral states option to tip nodes.

12 September 2006

A bug was identified by a user in which when saving the summary statistics from the morphology statistics window the individual transformation values are incorrectly printed - some are miss-aligned with the headers and some are missing. The total number of transformations is reported correctly as are all of the values in the window display. You will need to repeat all analyses that have used this data. The bug does not affect these values if they were saved to a file during the analysis. This bug DOES NOT AFFECT molecular analyses or data/results from any other type of analysis.

To check if your results are affected by this bug simply sum the individual transformation values. The value should be equal to the total number of transformations.

8 September 2006

Happily this news item does not deal with a bug but an enhancement to the website. The website now has a powerful search engine powered by the KScripts.com Ksearch search engine. To search the website select Search in the popup menu found in the top right of each page or the navigation bar at the bottom of the page.

7 September 2006

Fixed two important bugs. The first was introduced in the Beta 2.2 update and caused predictive simulations to crash. While it appears to not have effected other types of analysis users are strongly recommended to use the updated version and dispose of Beta 2.2 copies. This bug has been fixed as of version 2.3. The second bug was a problem associated with long runs calculating ancestral states. I believe this bug has been fixed and the analyses will run to completion. The bug caused the program to crash at the end of the run. If future problems occur with this type of analysis please submit a bug report refering to this problem. Fixed some minor potential bugs in which the user was allowed to select items from the main menu when an analysis was running causing crashes. In addition, the main menu would display the option to print a tree when no trees were in memory - this also would cause a program crash.

Some minor features have been added:
  1. Added a progress indicator and cancel button to the Calculate Ancestral states window.
  2. Added a timer that reports the amount to time before a character history analysis can be expected to finish.

23 August 2006

Fixed two minor bugs. The first bug involved the report a bug link in the alert window. The link was pointing to the old website and has now been fixed to point to the current website. The second bug involved a failure to display results of posterior ancestral state analysis. Some constraints would fail to report any results even though they had been successfully calculated. This bug was intermitten and has now been fixed. Any constraint with a least one occurence will be displayed in the results window. Both of these bugs are minor as they did not effect the quality of the results.

Added a number of minor interface options when calculating posterior ancestral states: 1) a progress indicator showing SIMMAP activity during the calculation, and 2) an option to log additional data when analyzing morphological characters. The log output contains information about the prior values of the discrete categories for the gamma and beta prior. These values are shown in the Log tab of the results window. This option has no effect when the data being analyzed is molecular.

I have changed the default value of the parameter (alpha) describing the beta prior. The previous value was set to 100 which gives, roughly, an equal probability of going from one state to the next (i.e., pi0 = 0.5). This is a fairly informative prior an excludes extreme values. The new parameter value is set to 1.0 which represents a flat, uninformative prior.

A note on SIMMAP's default values: SIMMAP has a set of default values for many of the options available to the user. These values are not an endorsement for their use. Please think critically about what values you are using during an analysis as the defaults may not be appropriate. This is most important when considering prior values on morphological character evolution (e.g., gamma rate, beta bias prior, and rescaling of the tree). Priors can be both useful and dangerous if miss-applied. You should check that the posterior from the prior is not stacking up against one end of the prior distribution (i.e., you are sampling only the largest or smallest values). If this is happening it is likely that you are excluding probable values and the prior is too restrictive.

19 May 2006

Fixed a minor bug that caused SIMMAP to crash when reading trees generated by the program BayesPhylogenies. See the Bug Reports page for additional information. Added additional magnification options in the TreeView window.

18 May 2006
The news comment on 15 April 2006 suggested that you could use zero length branches to emulate a polytomy in SIMMAP. At the time I believed, based on testing, that this would not cause problems. Unfortunately, it causes the program to crash. Therefore, I suggest not using this approach until I have figured out a solution that does not require a major re-working of how SIMMAP handles trees.

18 May 2006
As of version 1.0 Beta 2.0.9 you can now save any constraints you have created to a plist file. These can then be read back in at a later date. This should make creating constraints much more efficient, i.e., you only have to do this tedious task once. A constraints file could be created in a text editor but I reccommend that you use the SIMMAP interface to insure complaince with the file format and prevent the possibility of bugs. See the help documents on ancestral states and modifying trees for more information.

15 May 2006
I am trying to get rid of all the bugs (most recent can be seen here) and get the help documents completed. Too many options need to be documented and it takes a good chunk of my free time. Please email if something is undocumented and I will provide the requested details. Based on conversations with SIMMAP users I have realized that if the tree to be used contains polytomies it can be used in SIMMAP after first resolving the polytomies as zero length branches into a truly bifurcationg tree. In the past, I was concerned that this would cause an infinite loop in the program - I was wrong. After testing trees with polytomies, that have been resolved into a bifurcating structure using zero length branches, there seems to be no problem and this provides a unique way of performing stochastic character analysis on trees with polytomies (e.g., consensus trees from MrBayes). To facilitate this type of analysis I am providing a Python script to convert non-bifurcating trees into bifurcating trees that represent polytomies. See the new web page containing third-party scripts and programs here.

20 March 2006
The SIMMAP web site, www.simmap.com, is now being hosted at the University of Copenhagen, Center for Bioinformatics where I am currently a post-doctoral researcher. Many thanks to Mark Nellemann our excellent system administrator here in Copenhagen.

11 March 2006
The SIMMAP web site will be moving to a new physical location. This will have no effect on accessing the site at www.simmap.com. It is important that when you cite the SIMMAP web site that you use this web link and not the physical link seen in the browser address bar. SIMMAP is likely to move its physical location now and then. A note on the physical hosting location: SIMMAP is distributed by the author and not by a particular institution regardless of the fact that I have been kindly granted permission to host the web site at an Insititution.

2 February 2006
As with software web sites are user interfaces and need to be accessible and powerful. Hence, the SIMMAP web site, as you probably noticed, has been redesigned to enhance the user experience making it easier to access information about the SIMMAP software. In addition, the online Help Pages have been updated to be consistent and current with the most recent release of the SIMMAP software. I apologize for the past disconnect between the newest versions of SIMMAP and the available help in both the software distribution and available here.

How do you navigate the new cite? The web site can be navigated using the pull down menu at the top right of the site. To move to a particular topic on the site simply select a topic and there you go you will be taken there! I hope this helps and everybody reads the web page -- particularly, the Help Pages.

I have begun to expand the linking among pages (notice the underlined words). I believe this will help people move between related topics as intended by hyper-linking.

31 January 2006
Application software note accepted for publication in BMC Bioinformatics.

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