IDXL

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IDXL is a python based tool for computing species tree from a set of incongruent gene trees. For individual trees within the specified input treelist, following couplet based information are to be computed.

• Internode count between couplets, and
• Excess gene leaf count between individual couplets.

Two separate distance matrices are formed by computing the following statistic between individual couplets

• Average internode count.
• Filtered average (using mode based statistics) excess gene leaf count.

These couplet based distance matrices are then used in the adapted NJ method, to generate the species tree.

Input gene trees should be provided in a text file (list of gene trees) in either NEWICK or NEXUS format.

Output species tree is generated in the NEWICK format.

Input gene trees should be rooted. Otherwise default rooting settings will be employed. Gene trees can be incomplete and non binary as well.

Download executable (version 2.0)

IDXL.zip

README / MANUAL

User need to extract the zipped archieve. The executable name is IDXL, placed within the extracted directory.

• User Manual
• License

Sample Results

All the results published in the above manuscript are obtained using the command line options provided in the user manual.

For downloading results for various biological and simulated datasets, CLICK HERE --> RESULTS

Description of the results can be found in this document --> contents



For any queries, please contact:

• Sourya Bhattacharyya
  Department of Computer Science and Engineering
  Indian Institute of Technology Kharagpur
  Email: sourya DOT bhatta AT gmail DOT com
• Jayanta Mukherjee
  Department of Computer Science and Engineering
  Indian Institute of Technology Kharagpur
  Email: jay AT cse DOT iitkgp DOT ernet DOT in