Supplementary Table 2

Options used by IQ-TREE to control the search of an optimal model of SE

Option Consequence
-m MF ModelFinder
-m MFP Like MF but followed by tree reconstruction
-m TESTONLY Standard model selection (like jModelTest1 & ProtTest2)
-m TEST Like TESTONLY but followed by tree reconstruction
-m TESTMERGEONLY Select best-fit partition scheme (like PartitionFinder3)
-m TESTMERGE Like TESTMERGEONLY but followed by tree reconstruction
-m TESTNEWMERGEONLY Like TESTMERGEONLY but includes the new PDF model
-m TESTNEWMERGE Like TESTNEWMERGEONLY followed by tree reconstruction
-rcluster <percent> Percentage of partition pairs (relaxed clustering algorithm)
-mset program Restrict search to models supported by other programs (i.e.,
PhyML4, MrBayes5 or RAxML6)
-mset m1,...,mk Restrict search to models in a comma-separated list (e.g., -
mset WAG,LG,JTT)
-msub source Restrict search to AA models designed for specific sources
(i.e., nuclear, mitochondrial, chloroplast or viral)
-mfreq f1,...,fk Restrict search to using a list of state frequencies (default
protein: -mfreq FU,F; codon: -mfreq ,F1x4,F3x4,F)
-mrate r1,...,rk Restrict search to using a list of rate-across-sites models (e.g.
-mrate E,I,G,I+G,R)
-cmin <kmin> Min. # of rate categories for the PDF model (default: 2)
-cmax <kmax> Max. # of rate categories for the PDF model (default: 10)
-merit AIC|AICc|BIC Optimality criterion to use (default: all)
-mtree Performing full tree search for each model considered
-mredo Ignoring model results computed earlier (default: no)
-madd mx1,...,mxk List of mixture models to also consider
-mdef <nexus_file> A model definition NEXUS file (see Manual)

REFERENCES
1 Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. Nature Meth. 9, 772 (2012).
2 Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. Bioinformatics 27, 1164-1165
(2011).
3 Lanfear, R., Calcott, B., Ho, S. Y. W. & Guindon, S. Mol. Biol. Evol. 29, 1695-1701
(2012).
4 Guindon, S. et al. Syst. Biol. 59, 307-321 (2010).
5 Ronquist, F. et al. MrBayes 3.2: Syst. Biol. 61, 539-542 (2012).
6 Stamatakis, A. RAxML version 8: Bioinformatics 30, 1312-1313 (2014).

Nature Methods: doi:10.1038/nmeth.4285