Difference between revisions of "IQ-TREE"

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Latest revision as of 14:14, 30 July 2021

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

Note
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)