ImOSM - Imbed One Step Mutations into an alignment

ImOSM: Imbedding One Step Mutations into phylogenetic data.

Introduction:

ImOSM is a program to imbed intermittent evolution into a given alignment, where intermittent evolution refers to extra substitution(s) which are thrown on branch(es) of the tree to convert a site pattern of the alignment into another site pattern. Extra substitutions are modeled by the one step mutation (OSM) matrix. Thus, ImOSM actually Imbeds intermittent One Step Mutations into the alignment.

Methods:

The method is described in the following article (section ImOSM method):

Minh Anh Thi Nguyen, Tanja Gesell and Arndt von Haeseler, ImOSM: Intermittent Evolution and Robustness of Phylogenetic Methods. Mol. Biol. Evol., 29, 663-673. (free reprint, DOI: 10.1093/molbev/msr220, PMID: 21940641)

Availability:

The program is written in C++ and available free of charge. The executable file currently works under Linux platform. Binary files for MacOS and Windows systems can be compiled from the source code provided.

Version history:

Sep 02, 2011: Some code refinement to the sampling from discrete distribution in order to save computation time when the number of categories as well as the number of samples are large.
June 2011: The first version was launched.

Note:

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.