Oral Presentation Society for Molecular Biology and Evolution Conference 2016

IQ-TREE: efficient phylogenomic software for maximum likelihood analysis (#160)

Arndt von Haeseler 1 , Olga Chernomor 1 , Bui Quang Minh 1 , Lam-Tung Nguyen 1 , Heiko A Schmidt 1 , Jana Trifinopoulos 1
  1. University of Vienna, Vienna, VIENNA, Austria

We present IQ-TREE, the successor of the TREE-PUZZLE and IQPNNI software, as an efficient and versatile phylogenomic tool for maximum likelihood analysis of large alignments. IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) and a wide range of evolutionary models including mixture and partition models. IQ-TREE performs fast model selection, partition scheme finding, likelihood mapping, efficient tree reconstruction, terrace aware phylogenomic inference, ultrafast bootstrapping, branch tests, and tree topology tests. IQ-TREE supports parallel computation and provides check-pointing to restart phylogenetic analysis if the original run was interrupted. IQ-TREE infers usually higher likelihood trees than RAxML and PhyML while requiring similar amount of computing time. However, the performance of all three likelihood tools depends on the data set. Thus, it is useful to run several programs.

IQ-TREE is open-source, it supports all major platforms (Windows, Mac OSX, Linux) and is freely available from http://www.cibiv.at/software/iqtree. For novice users a user-friendly web server is available at http://iqtree.cibiv.univie.ac.at.