Journal of Molecular Evolution

, Volume 85, Issue 1–2, pp 57–78 | Cite as

IDXL: Species Tree Inference Using Internode Distance and Excess Gene Leaf Count

Original Article


We propose an extension of the distance matrix methods NJst and ASTRID to infer species trees from incongruent gene trees having Incomplete Lineage Sorting. Both approaches consider the average internode distance (ID) between individual taxa pairs as the distance measure. The measure ID does not use the root of a tree, and thus may not always infer the relative position of a taxon with respect to the root. We define a novel distance measure excess gene leaf count (XL) between individual couplets. The XL measure is computed using the root of a tree. It is proved to be additive, and is shown to infer the relative order of divergence among individual couplets better. We propose a novel method IDXL which uses both the XL and ID measures for species tree construction. IDXL is shown to perform better than NJst and other distance matrix approaches for most of the biological and simulated datasets. Having the same computational complexity as NJst, IDXL can be applied for species tree inference on large-scale biological datasets.


Gene tree/species tree incongruence Deep coalescence (DC) or Incomplete Lineage Sorting (ILS) Neighbor Joining Internode distance Excess gene leaf Bootstrapping 



The first author acknowledges Tata Consultancy Services (TCS) for providing the research scholarship. We acknowledge the anonymous reviewers for their insightful comments and suggestions towards improvement of this work.

Supplementary material

239_2017_9807_MOESM1_ESM.pdf (1.8 mb)
Supplementary material 1 (pdf 1810 KB)


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Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  1. 1.Department of Computer Science and EngineeringIndian Institute of Technology KharagpurKharagpurIndia

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