IQ-TREE

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Description

iq-tree website

IQ-Tree is a very efficient maximum likelihood phylogenetic software.

Required Modules

Parallel (MPI)

gcc
openmpi
iq-tree

System Variables

HPC_IQ-TREE_DIR - installation directory
HPC_IQ-TREE_BIN - executable directory

Additional Information

There is no executable named 'iqtree' in this package starting with iq-tree/1.5.3. Use either iqtree-mpi or iqtree-omp-mpi depending on whether an MPI or a hybrid job is to be run.

Citation

If you publish research that uses iq-tree you have to cite it as follows:

To cite IQ-TREE please use:

Lam Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler, and Bui Quang Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol., 32, 268-274. (DOI: 10.1093/molbev/msu300)

To cite the ultrafast bootstrap (UFBoot) please use:

Bui Quang Minh, Minh Anh Thi Nguyen, and Arndt von Haeseler (2013) Ultrafast approximation for phylogenetic bootstrap. Mol. Biol. Evol., 30:1188-1195. (DOI: 10.1093/molbev/mst024)

IQ-TREE can use PLL for likelihood computations, if you use "-pll" option please cite:

T. Flouri, F. Izquierdo-Carrasco, D. Darriba, A.J. Aberer, L.-T. Nguyen, B.Q. Minh, A. von Haeseler, and A. Stamatakis (2014) The phylogenetic likelihood library. Syst. Biol., in press. (DOI: 10.1093/sysbio/syu084)