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COSPEDTree (Couplet based Phylogenetic Supertree algorithm, using equivalence partitioning and taxa set formation)

(Note: a much efficient and of lower running time version, COSPEDBTree (or COSPEDTree-II) is available in GitHub. user may use that version).

COSPEDTree is a python package to compute phyloegentic supertree from input trees having conflicting topologies and possibly overlapping taxa subsets. The tool proposes phylogenetic relations among individual couplets, and aims to resolve the topological conflicts via selecting the most frequent couplet specific relations in an iterative fashion. The selected couplet relations are assembled to form a directed acyclic graph (DAG), from which the final supertree is generated.

Input

Phylogenetic trees with conflicting topologies and possibly overlapping taxa subsets. Input trees can be either in NEWICK format or in NEXUS format. However, all input trees should have identical input formats.

Output

Output tree is generated in the NEWICK format.

Dependencies / Installation Requirements

COSPEDTree is developed in Linux Systems (Ubuntu 12.04), using Python 2.7. User needs to install following before using this package:

  1. Python 2.7 (available in Ubuntu, by default).

Note: Current implementation of COSPEDTree do not support Python 3. A future release would cover it.

  1. Dendropy ( available on the link: https://pythonhosted.org/DendroPy/ )

Note: we have used version 3.12.0 for implementation. Future releases of Dendropy are to be tested and incorporated in a separate release.

  1. Numpy ( available on the link: http://www.numpy.org/ )

Available via pip (python software installer tool).

Execution

COSPEDTree.py is the main executable. Its execution is done by the following command:

python COSPEDTree.py [options]

Details of the options are mentioned below:

-h, --help

show this help message and exit

-I INP_FILENAME, --INPFILE=INP_FILENAME

Input file containing input set of trees.

-p INP_FILE_FORMAT, --inpform=INP_FILE_FORMAT

1 - input file format is NEWICK (default)
2 - input file format is NEXUS       
USER MUST PROVIDE either p = 1 or 2

-c, --costupdate

Boolean option: toggles the default (FALSE) settings.
if TRUE, updates the cost settings of individual relations after each iteration. 
Recommended: TRUE
May incur high running time for large trees.

Example of a command:

python COSPEDTree.py -I source_tree_input.txt -p1 > out.txt (redirecting the console)

Output description

Output log and detailed execution are printed in console.

A file "output_supertree_newick.tre" is created in the current directory, which contains the generated supertree.

At the end of the output console, performance metrics like SUMFP, sumFN, between the output supertree and the input trees are also printed.

Citation

Upon using this package, users need to cite the following articles:

  1. Sourya Bhattacharyya, and Jayanta Mukherjee, "COSPEDTree: COuplet Supertree by Equivalence Partitioning of taxa set and DAG formation", IEEE/ACM Transactions on Computational Biology and Bioinformatics, pp. 1-1, doi: http://doi.ieeecomputersociety.org/10.1109/TCBB.2014.2366778

  2. Sourya Bhattacharyya, and Jayanta Mukhopadhyay, "COuplet Supertree by Equivalence Partitioning of taxa set and DAG formation", Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), Newport, California, September 2014, pages 259-268.

For any queries, please contact

Sourya Bhattacharyya

La Jolla Institute for Allergy and Immunology

La Jolla, CA, 92037, USA

[email protected]