Center for Integrative Bioinformatics Vienna
Max F. Perutz Laboratories
Dr. Bohr Gasse 9
A-1030 Vienna, Austria

MISFITS: Evaluating the goodness of fit between a phylogenetic model and an alignment.


  • April 21, 2011: Updated MANUAL provides detailed information how to compute the confidence interval.
  • August 11, 2010: Binary for Windows system is provided, though not carefully tested yet.
  • August 10, 2010: Binary and bash scripts for MacOS X are provided.


MISFITS is a program to evaluate the goodness of fit of a model to an alignment in phylogeny reconstruction. It offers a look back at the alignment to pinpoint to site patterns that do not fit to the model and the resulting tree (thereafter referred to as the tree-model). MISFITS then introduces a number of extra-substitutions on the tree, in a parsimonious manner to fit these site patterns in to the tree-model. These extra-substitutions plus the evolutionary model will then fully explain the alignment. Thus, the number of extra-substitutions may be interpreted as a measure to evaluate the goodness of fit of the model to the alignment: the less the number, the better the fit.


The method is described in the following article: A brief description of the method is as follows:
  1. Count the observed frequency of patterns in the alignment.
  2. Compute pattern likelihood under the model and the inferred tree.
  3. Determine the set of over-represented patterns D+ and the set of under-represented patterns D-.
  4. For all pairs of patterns (p, p'), p ∈ D+, p' ∈ D-, compute the minimal number of extra-substitutions to convert p into p'.
  5. Select a matching between patterns in D+ and D- such that the total number of extra-substitutions is minimal.
  6. Map the extra-substitutions on the tree.
  7. Determine the significance of the number of extra-substitutions computed at step 5.


  • For step 1-6: The program is written in C++ and available free of charge. The executable file currently works under Unix platform (Linux and MacOS X systems) as well as Windows system.
  • For step 7: Since it depends on the simulation and tree reconstruction programs that users want to use, we provide a number of bash scripts running on Unix systems to carry out this task with: SEQ-GEN for simulation and PHYML for tree reconstruction. Users may modify these scripts to use other programs instead as well as to use misfits with different options.
  • Refer to download for the source code, program manual, binary file of misfits and the bash scripts.

External programs required:

  • For step 1-6: the MISFITS program requires TREE-PUZZLE to compute likelihood of the patterns (written in a phylip format alignment) given the tree and the model with the corresponding parameter's values. Please make sure that the executable file of TREE-PUZZLE is named puzzle.
  • For step 7: a simulator and a tree-reconstruction program are needed. If you use the bash scripts we provide, you need SEQ-GEN and PHYML packages and the executable files should be named seq-gen and PhyML_3.0, respectively.
  • Make sure that you use the correct binaries of these external programs, i.e. compatible with your system (Linux, MacOS, Windows).

Version history:

  • March 2010: The first version misfits-1.0 was launched.


Please read the manual carefully if you try our program the first time. If you encounter bugs, please report to minh.anh.nguyen(AT)univie.ac.at together with the log files.


Type Links
Manual misfits_manual.pdf
Source code misfits-1.0.tar.gz
Binary files for Linux system
(misfits-1.0, including 32-bit-binary)
Binary files for MacOS X system
Binary files for Windows system
Example example.tar.gz
Bash scripts for Unix (Linux and MacOS X) Unix-phyml-misfits-1.0.tar.gz

Printable version of: http://www.cibiv.at/software/misfits/index.html

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