Manual

Last update: Aug 1, 2017, Contributors: Jana Trifinopoulos, Minh Bui

Substitution models

All common substitution models and usages.

IQ-TREE supports a wide range of substitution models, including advanced partition and mixture models. This guide gives a detailed information of all available models.

TIP: If you do not know which model to use, simply run IQ-TREE with the standard model selection (-m TEST option) or the new ModelFinder (-m MFP). It automatically determines best-fit model for your data.

DNA models

Base substitution rates

IQ-TREE includes all common DNA models (ordered by complexity):

ModeldfExplanationCode
JC or JC690Equal substitution rates and equal base frequencies (Jukes and Cantor, 1969).000000
F813Equal rates but unequal base freq. (Felsenstein, 1981).000000
K80 or K2P1Unequal transition/transversion rates and equal base freq. (Kimura, 1980).010010
HKY or HKY854Unequal transition/transversion rates and unequal base freq. (Hasegawa, Kishino and Yano, 1985).010010
TN or TN935Like HKY but unequal purine/pyrimidine rates (Tamura and Nei, 1993).010020
TNe2Like TN but equal base freq.010020
K81 or K3P2Three substitution types model and equal base freq. (Kimura, 1981).012210
K81u5Like K81 but unequal base freq.012210
TPM22AC=AT, AG=CT, CG=GT and equal base freq.121020
TPM2u5Like TPM2 but unequal base freq.121020
TPM32AC=CG, AG=CT, AT=GT and equal base freq.120120
TPM3u5Like TPM3 but unequal base freq.120120
TIM6Transition model, AC=GT, AT=CG and unequal base freq.012230
TIMe3Like TIM but equal base freq.012230
TIM26AC=AT, CG=GT and unequal base freq.121030
TIM2e3Like TIM2 but equal base freq.121030
TIM36AC=CG, AT=GT and unequal base freq.120130
TIM3e3Like TIM3 but equal base freq.120130
TVM7Transversion model, AG=CT and unequal base freq.412310
TVMe4Like TVM but equal base freq.412310
SYM5Symmetric model with unequal rates but equal base freq. (Zharkihk, 1994).123450
GTR8General time reversible model with unequal rates and unequal base freq. (Tavare, 1986).123450

The last column Code is a 6-digit code definining the equality constraints for 6 relative substitution rates: A-C, A-G, A-T, C-G, C-T and G-T. 010010 means that A-G rate is equal to C-T rate (corresponding to 1 in the code) and the remaining four substitution rates are equal (corresponding to 0 in the code). Thus, 010010 is equivalent to K80 or HKY model (depending on whether base frequencies are equal or not). 123450 is equivalent to GTR or SYM model as there is no restriction defined by such 6-digit code.

Moreover, IQ-TREE supports arbitrarily restricted DNA model via a 6-digit code, e.g. with option -m 120120+G.

NOTE: The last digit in this code must always be 0. It corresponds to G-T rate which is always equal to 1.0 for convenience because the rates are relative.

If users want to fix model parameters, append the model name with a curly bracket {, followed by the comma-separated rate parameters, and a closing curly bracket }. For example, GTR{1.0,2.0,1.5,3.7,2.8} specifies 6 substitution rates A-C=1.0, A-G=2.0, A-T=1.5, C-G=3.7, C-T=2.8 and G-T=1.0.

Another example is for model TIM2 that has the 6-digit code 121030. Thus, TIM2{4.39,5.30,12.1} means that A-C=A-T=4.39 (coded 1), A-G=5.30 (coded 2), C-T=12.1 (coded 3) and C-G=G-T=1.0 (coded 0). This is, in turn, equivalent to specifying GTR{4.39,5.30,4.39,1.0,12.1}.

Base frequencies

Users can specify three different kinds of base frequencies:

FreqTypeExplanation
+FEmpirical base frequencies. This is the default if the model has unequal base freq.
+FQEqual base frequencies.
+FOOptimized base frequencies by maximum-likelihood.

For example, GTR+FO optimizes base frequencies by ML whereas GTR+F (default) counts base frequencies directly from the alignment.

Finally, users can fix base frequencies with e.g. GTR+F{0.1,0.2,0.3,0.4} to fix the corresponding frequencies of A, C, G and T (must sum up to 1.0).

Lie Markov models

Starting with version 1.6, IQ-TREE supports a series of Lie Markov models (Woodhams et al., 2015), many of which are non-reversible models. Lie Markov models have a consistent property, which is lacking in other common models such as GTR. The following table shows the list of all Lie Markov models (the number before . in the name shows the number of parameters of the model):

ModelRev?FreqNote
1.1Yes0equiv. to JC
2.2bYes0equiv. to K2P
3.3aYes0equiv. to K3P
3.3bNo0 
3.3cYes0equiv. to TNe
3.4Yes1 
4.4aYes3equiv. to F81
4.4bYes1 
4.5aNo1 
4.5bNo1 
5.6aNo0 
5.6bNo3 
5.7aNo2 
5.7bNo0 
5.7cNo0 
5.11aNo2 
5.11bNo0 
5.11cNo0 
5.16No1 
6.6No1equiv. to STRSYM (strand symmetric model)
6.7aNo3F81+K3P
6.7bNo3 
6.8aNo3 
6.8bNo1 
6.17aNo1 
6.17bNo1 
8.8No3 
8.10aNo3 
8.10bNo1 
8.16No3 
8.17No3 
8.18No3 
9.20aNo2 
9.20bNo0Doubly stochastic
10.12No3 
10.34No3 
12.12No3equiv. to UNREST (unrestricted model)

Column Rev? shows whether the model is reversible or not. Column Freq shows the number of free base frequencies. 0 means equal base frequency; 1 means f(A)=f(G) and f(C)=f(T); 2 means f(A)+f(G)=0.5=f(C)+f(T); 3 means unconstrained frequencies.

All Lie Markov models can have one of the following prefices:

PrefixMeaning
RYpurine-pyrimidine pairing (default)
WSweak-strong pairing
MKaMino-Keto pairing

Protein models

Amino-acid exchange rate matrices

IQ-TREE supports all common empirical amino-acid exchange rate matrices (alphabetical order):

ModelExplanation
BLOSUM62BLOcks SUbstitution Matrix (Henikoff and Henikoff, 1992). Note that BLOSUM62 is not recommended as it was designed mainly for sequence alignments.
cpREVchloroplast matrix (Adachi et al., 2000).
DayhoffGeneral matrix (Dayhoff et al., 1978).
DCMutRevised Dayhoff matrix (Kosiol and Goldman, 2005).
FLUInfluenza virus (Dang et al., 2010).
HIVbHIV between-patient matrix HIV-Bm (Nickle et al., 2007).
HIVwHIV within-patient matrix HIV-Wm (Nickle et al., 2007).
JTTGeneral matrix (Jones et al., 1992).
JTTDCMutRevised JTT matrix (Kosiol and Goldman, 2005).
LGGeneral matrix (Le and Gascuel, 2008).
mtARTMitochondrial Arthropoda (Abascal et al., 2007).
mtMAMMitochondrial Mammalia (Yang et al., 1998).
mtREVMitochondrial Verterbrate (Adachi and Hasegawa, 1996).
mtZOAMitochondrial Metazoa (Animals) (Rota-Stabelli et al., 2009).
PoissonEqual amino-acid exchange rates and frequencies.
PMBProbability Matrix from Blocks, revised BLOSUM matrix (Veerassamy et al., 2004).
rtREVRetrovirus (Dimmic et al., 2002).
VTGeneral matrix (Mueller and Vingron, 2000).
WAGGeneral matrix (Whelan and Goldman, 2001).
GTR20General time reversible models with 190 rate parameters. *WARNING: Be careful when using this parameter-rich model as parameter estimates might not be stable, especially when not having enough phylogenetic information (e.g. not long enough alignments). *

Protein mixture models

IQ-TREE also supports a series of protein mixture models:

ModelExplanation
C10 to C6010, 20, 30, 40, 50, 60-profile mixture models (Le et al., 2008a) as variants of the CAT model (Lartillot and Philippe, 2004) for ML. Note that these models assume Poisson AA replacement and implicitly include a Gamma rate heterogeneity among sites.
EX2Two-matrix model for exposed/buried AA sites (Le et al., 2008b).
EX3Three-matrix model for highly exposed/intermediate/buried AA sites (Le et al., 2008b).
EHOThree-matrix model for extended/helix/other sites (Le et al., 2008b).
UL2, UL3Unsupervised-learning variants of EX2 and EX3, respectively.
EX_EHOSix-matrix model combining EX2 and EHO (Le and Gascuel, 2010).
LG4MFour-matrix model fused with Gamma rate heterogeneity (Le et al., 2012).
LG4XFour-matrix model fused with FreeRate heterogeneity (Le et al., 2012).
CF4Five-profile mixture model (Wang et al., 2008).

One can even combine a protein matrix with a profile mixture model like:

  • LG+C20: Applying LG matrix instead of Poisson for all 20 classes of AA profiles and a Gamma rate heterogeneity.
  • LG+C20+F: Applying LG matrix for 20 classes plus the 21th class of empirical AA profile (counted from the current data) and Gamma rate heterogeneity.
  • JTT+CF4+G: Applying JTT matrix for all 5 classes of AA profiles and Gamma rate heteorogeneity.

Moreover, one can override the Gamma rate by FreeRate heterogeneity:

  • LG+C20+R4: Like LG+C20 but replace Gamma by FreeRate heterogeneity.

User-defined empirical protein models

If the matrix name does not match any of the above listed models, IQ-TREE assumes that it is a file containing AA exchange rates and frequencies in PAML format. It contains the lower diagonal part of the matrix and 20 AA frequencies, e.g.:

0.425093 
0.276818 0.751878 
0.395144 0.123954 5.076149 
2.489084 0.534551 0.528768 0.062556 
0.969894 2.807908 1.695752 0.523386 0.084808 
1.038545 0.363970 0.541712 5.243870 0.003499 4.128591 
2.066040 0.390192 1.437645 0.844926 0.569265 0.267959 0.348847 
0.358858 2.426601 4.509238 0.927114 0.640543 4.813505 0.423881 0.311484 
0.149830 0.126991 0.191503 0.010690 0.320627 0.072854 0.044265 0.008705 0.108882 
0.395337 0.301848 0.068427 0.015076 0.594007 0.582457 0.069673 0.044261 0.366317 4.145067 
0.536518 6.326067 2.145078 0.282959 0.013266 3.234294 1.807177 0.296636 0.697264 0.159069 0.137500 
1.124035 0.484133 0.371004 0.025548 0.893680 1.672569 0.173735 0.139538 0.442472 4.273607 6.312358 0.656604 
0.253701 0.052722 0.089525 0.017416 1.105251 0.035855 0.018811 0.089586 0.682139 1.112727 2.592692 0.023918 1.798853 
1.177651 0.332533 0.161787 0.394456 0.075382 0.624294 0.419409 0.196961 0.508851 0.078281 0.249060 0.390322 0.099849 0.094464 
4.727182 0.858151 4.008358 1.240275 2.784478 1.223828 0.611973 1.739990 0.990012 0.064105 0.182287 0.748683 0.346960 0.361819 1.338132 
2.139501 0.578987 2.000679 0.425860 1.143480 1.080136 0.604545 0.129836 0.584262 1.033739 0.302936 1.136863 2.020366 0.165001 0.571468 6.472279 
0.180717 0.593607 0.045376 0.029890 0.670128 0.236199 0.077852 0.268491 0.597054 0.111660 0.619632 0.049906 0.696175 2.457121 0.095131 0.248862 0.140825 
0.218959 0.314440 0.612025 0.135107 1.165532 0.257336 0.120037 0.054679 5.306834 0.232523 0.299648 0.131932 0.481306 7.803902 0.089613 0.400547 0.245841 3.151815 
2.547870 0.170887 0.083688 0.037967 1.959291 0.210332 0.245034 0.076701 0.119013 10.649107 1.702745 0.185202 1.898718 0.654683 0.296501 0.098369 2.188158 0.189510 0.249313 

0.079066 0.055941 0.041977 0.053052 0.012937 0.040767 0.071586 0.057337 0.022355 0.062157 0.099081 0.064600 0.022951 0.042302 0.044040 0.061197 0.053287 0.012066 0.034155 0.069147 

(This is an example of an LG matrix taken from PAML package). Note that the amino-acid order in this file is:

 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val

Amino-acid frequencies

By default, AA frequencies are given by the model. Users can change this with:

FreqTypeExplanation
+Fempirical AA frequencies from the data.
+FOML optimized AA frequencies from the data.
+FQEqual AA frequencies.

Users can also specify AA frequencies with, e.g.:

+F{0.079066,0.055941,0.041977,0.053052,0.012937,0.040767,0.071586,0.057337,0.022355,0.062157,0.099081,0.064600,0.022951,0.042302,0.044040,0.061197,0.053287,0.012066,0.034155,0.069147}

(Example corresponds to the AA frequencies of the LG matrix).

Codon models

To apply a codon model one should use the option -st CODON to tell IQ-TREE that the alignment contains protein coding sequences (otherwise, IQ-TREE thinks that it contains DNA sequences and will apply DNA models). This implicitly applies the standard genetic code. You can change to an other genetic code by appending the appropriate ID to the CODON keyword:

CodeGenetic code meaning
CODON1The Standard Code (same as -st CODON)
CODON2The Vertebrate Mitochondrial Code
CODON3The Yeast Mitochondrial Code
CODON4The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
CODON5The Invertebrate Mitochondrial Code
CODON6The Ciliate, Dasycladacean and Hexamita Nuclear Code
CODON9The Echinoderm and Flatworm Mitochondrial Code
CODON10The Euplotid Nuclear Code
CODON11The Bacterial, Archaeal and Plant Plastid Code
CODON12The Alternative Yeast Nuclear Code
CODON13The Ascidian Mitochondrial Code
CODON14The Alternative Flatworm Mitochondrial Code
CODON16Chlorophycean Mitochondrial Code
CODON21Trematode Mitochondrial Code
CODON22Scenedesmus obliquus Mitochondrial Code
CODON23Thraustochytrium Mitochondrial Code
CODON24Pterobranchia Mitochondrial Code
CODON25Candidate Division SR1 and Gracilibacteria Code

(The IDs follow the specification at http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).

Codon substitution rates

IQ-TREE supports several codon models:

ModelExplanation
MGNonsynonymous/synonymous (dn/ds) rate ratio (Muse and Gaut, 1994).
MGKLike MG with additional transition/transversion (ts/tv) rate ratio.
MG1KTS or MGKAP2Like MG with a transition rate (Kosiol et al., 2007).
MG1KTV or MGKAP3Like MG with a transversion rate (Kosiol et al., 2007).
MG2K or MGKAP4Like MG with a transition rate and a transversion rate (Kosiol et al., 2007).
GYNonsynonymous/synonymous and transition/transversion rate ratios (Goldman and Yang, 1994).
GY1KTS or GYKAP2Like GY with a transition rate (Kosiol et al., 2007).
GY1KTV or GYKAP3Like GY with a transversion rate (Kosiol et al., 2007).
GY2K or GYKAP4Like GY with a transition rate and a transversion rate (Kosiol et al., 2007).
ECMK07 or KOSI07Empirical codon model (Kosiol et al., 2007).
ECMrestRestricted version of ECMK07 that allows only one nucleotide exchange.
ECMS05 or SCHN05Empirical codon model (Schneider et al., 2005).

The last three models (ECMK07, ECMrest or ECMS05) are called empirical codon models, whereas the others are called mechanistic codon models.

Moreover, IQ-TREE supports combined empirical-mechanistic codon models using an underscore separator (_). For example:

  • ECMK07_GY2K: The combined ECMK07 and GY2K model, with the rate entries being multiplication of the two corresponding rate matrices.

Thus, there can be many such combinations.

If the model name does not match any of the above listed models, IQ-TREE assumes that it is a file containing codon exchange rates and frequencies in PAML format. It contains the lower diagonal part of the matrix and codon frequencies. For an example, see http://www.ebi.ac.uk/goldman/ECM/.

NOTE: Branch lengths under codon models are interpreted as number of nucleotide substitutions per codon site. Thus, they are typically 3 times longer than under DNA models.

Codon frequencies

IQ-TREE supports the following codon frequencies:

FreqTypeExplanation
+FEmpirical codon frequencies counted from the data.
+FQEqual codon frequencies.
+F1X4Unequal nucleotide frequencies but equal nt frequencies over three codon positions.
+F3X4Unequal nucleotide frequencies and unequal nt frequencies over three codon positions.

If not specified, the default codon frequency will be +F3X4 for MG-type models, +F for GY-type models and given by the model for empirical codon models.

Binary and morphological models

The binary alignments should contain state 0 and 1, whereas for morphological data, the valid states are 0 to 9 and A to Z.

ModelExplanation
JC2Jukes-Cantor type model for binary data.
GTR2General time reversible model for binary data.
MKJukes-Cantor type model for morphological data.
ORDEREDAllowing exchange of neighboring states only.

Except for GTR2 that has unequal state frequencies, all other models have equal state frequencies.

TIP: If morphological alignments do not contain constant sites (typically the case), then an ascertainment bias correction model (+ASC) should be applied to correct the branch lengths for the absence of constant sites.

Ascertainment bias correction

An ascertainment bias correction (+ASC) model (Lewis, 2001) should be applied if the alignment does not contain constant sites (such as morphological or SNPs data). For example:

  • MK+ASC: For morphological data.
  • GTR+ASC: For SNPs data.

+ASC will correct the likelihood conditioned on variable sites. Without +ASC, the branch lengths might be overestimated.

Rate heterogeneity across sites

IQ-TREE supports all common rate heterogeneity across sites models:

RateTypeExplanation
+Iallowing for a proportion of invariable sites.
+Gdiscrete Gamma model (Yang, 1994) with default 4 rate categories. The number of categories can be changed with e.g. +G8.
+I+Ginvariable site plus discrete Gamma model (Gu et al., 1995).
+RFreeRate model (Yang, 1995; Soubrier et al., 2012) that generalizes the +G model by relaxing the assumption of Gamma-distributed rates. The number of categories can be specified with e.g. +R6 (default 4 categories if not specified). The FreeRate model typically fits data better than the +G model and is recommended for analysis of large data sets.
+I+Rinvariable site plus FreeRate model.

TIP: The new ModelFinder (-m MFP option) tests the FreeRate model, whereas the standard procedure (-m TEST) does not.

Users can fix the parameters of the model. For example, +I{0.2} will fix the proportion of invariable sites (pinvar) to 0.2; +G{0.9} will fix the Gamma shape parameter (alpha) to 0.9; +I{0.2}+G{0.9} will fix both pinvar and alpha. To fix the FreeRate model parameters, use the syntax +Rk{w1,r1,...,wk,rk} (replacing k with the number of categories). Here, w1, ..., wk are the weights and r1, ..., rk the rates for each category.

NOTE: For the +G model IQ-TREE implements the mean approximation approach (Yang, 1994). The same is done in RAxML and PhyML. However, some programs like TREE-PUZZLE implement the median approximation approach, which makes the resulting log-likelihood not comparable. IQ-TREE can change to this approach via the -gmedian option.