Frequently Asked Questions

  1. Q. Can I analyze an amino acid (protein) data set in SIMMAP 1.5?

    A. No. However, you can analyze patterns of amino acid evolution using a nucleotide data set with coding structure enforced and the residues inferred from a chosen genetic code.

  2. Q. Can I analyze a data set that has both nucleotide and morphological data in SIMMAP 1.5?

    A. No. SIMMAP 1.5 only supports single datatypes in a file.

  3. Q. I am performing an ASR analysis and have not rooted the tree. However, the results report values for the root. Is the analysis rooted?

    A. No. All the models used in SIMMAP 1.5 are reversible and therefore when calculating ancestral states it matters not where the root is. If you are interested in the root then these will be useful. If you are not you can ignore them. The reported root values reflect how the tree is displayed and will be arbitrary unless the tree(s) have been rooted.

  4. Q. How do I cite an analysis using SIMMAP 1.5?

    A. You should cite the Software Note for version 1.0 that was published in the journal BMC Bioinformatics. An example of the citation is:

    Bollback J. P. (2006) SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 7:88.

    In addition, you should cite in the text of the manuscript the full version used for the analysis (e.g., SIMMAP Version 1.5).

  5. Q. Is SIMMAP 1.5 open source?

    A. No

  6. Q. Are you planning to release a GUI version of SIMMAP 1.5 for Windows (X Windows, Linux)?

    A. No. However, you can run the more feature rich command line version of SIMMAP 2.0 once it is finally released.

  7. Q. Will SIMMAP 1.5 work with multifurcating trees, such as a consensus tree?

    A. Yes, SIMMAP 1.5 now supports multifurcations.

  8. Q. How do I convert my Nexus files and Mrbayes files to the new Xml format used by SIMMAP 1.5?

    A. I have provided a simple utliity program called Nex2Xml for this purpose. You can download it here.

  9. Q. Can I use SIMMAP 1.5 for research being conducted for commercial purposes or otherwise for profit (including patent gain) research?

    A. No, you will need to purchase a user license (see the License for more information on the "Permitted License Uses and Restrictions"). For more information please send an email to,

  10. Q. How many morphological character states can SIMMAP 1.5 handle?

    A. 7, coded from 0 to 6.

  11. Q. Are the default values in SIMMAP 1.5 the recommended values?

    A. No. You should explore different scenarios for your analysis before proceeding with the final analysis.

  12. Q. What priors should I use in my analysis of morphological/standard characters?

    A. Unfortunately, no simple answer exists as it depends on many factors. However, SIMMAP 1.5 now supports a statistical approach to selecting priors. Check out the following link for more information: Morphology Priors

  13. Q. Are the ancestral states reconstructed in SIMMAP 1.5 the marginal or the joint posterior probability?

    A. When performing an Ancestral states analysis the results are marginal. For all other analyses they use a sampling from the joint distribution.

  14. Q. Does SIMMAP 1.5 enforce a single prior for all morphological/standard characters?

    A. No. This was a constraint in the previous version and has been relaxed in the new version; each character can have a different set of morphological priors.

  15. Q. If the documents on this web site don't answer my questions who can I ask?

    A. If your queries are not answered on the web site you can always email,, for more help.