SVDquartets: Singular Value Decomposition Scores for Species Quartets



SVDquartets is now implemented in PAUP*! You can download the latest version of the software here: http://people.sc.fsu.edu/~dswofford/paup_test/. All analysis should be carried out using this new version of the software. The earlier versions are maintained below for any analyses that pre-dated the implementation of the method in PAUP*.


Descriptions of the method can be found in the following references:
Published analyses that use the method should also cite PAUP*.






Older Versions:

Version 1.0


Laura S. Kubatko and Julia Chifman
Department of Statistics
The Ohio State University
Columbus, OH 43210
lkubatko@stat.osu.edu


Copyright 2014 by Laura Kubatko. This software is provided "as is" without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and documentation, is distributed free of charge. This software is covered under the Gnu GPL (General Public License).

The method is described in the following papers:

Chifman, J. and L. Kubatko. 2014. Quartet inference from SNP data under the coalescent, Bioinformatics, 30(23): 3317-3324.

Chifman, J. and L. Kubatko. 2014. Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, available on arXiv.


About the Program

SVDquartets is a program to compute a score based on singular value decomposition of a matrix of site pattern frequencies corresponding to a split on a phylogenetic tree. These quartet scores can be used to select the best-supported topology for quartets of taxa, which in turn can be used to infer the species phylogeny using quartet methods.



Download:


Release notes:


Instructions:
  1. Compile the programs from the source codes:
    (a) Copy "Makefile_scores" to "Makefile" and type "make".
    (b) Copy "Makefile_quartets" to "Makefile" and type "make".
  2. Place your data in PHYLIP format in a file called "data.phy" (an example is placed in the file snakes.phy in the downloaded files).
  3. Check to see that the file "splits" (included in the download) is in the current directory
  4. Issue the command " ./SVDquartets ".
  5. The output file is called "quartets.out". This is the file that would be used in the quartet assembly programs. It is formatted correctly for Quartet MaxCut, but may need to be modified for other programs.


Acknowledgements

Continued development of SVDquartets is based upon work supported by the National Science Foundation under Grant DMS 1106706. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.



Contact Info

Questions or comments concerning the program can be e-mailed to me at lkubatko@stat.osu.edu. Please also e-mail me if you'd like to be advised when updated versions of the program become available.




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