How to find a best fit model using IQ-TREE?

Dr. Muniba Faiza
2 Min Read

Previously, we have provided an installation tutorial for IQ-TREE on Ubuntu. In this article, we are going to perform model selection for a dataset using the standalone tool of IQ-TREE.

ModelFinder [1] of IQ-TREE helps to identify the best fit model for data. It supports several substitution models for DNA, protein, codon, and binary alignment.

Follow the steps given below:

  • Align your sequences using any alignment software or a webserver such as Clustal, Muscle, and MAFFT.
  • Save the alignment in Phylip, FASTA, MSF, NEXUS, or Clustal format.
  • Now open a terminal by pressing Ctrl+Alt+T.
  • Paste the following command:
    $ iqtree -s aligned_seqs.fasta -m <model_name>
    Here, -m refers to the model name such as TIM2+I+G, JC, TPM, WAG, and so on. You can select a model from here.
  • If you do not know an appropriate model for your data then use the following command to test all models:
    $ iqtree -s aligned_seqs.fasta -m MFP
  • If you want to resemble jModelTest/ ProtTest, then use the following command:
    $ iqtree -s aligned_seqs.fasta -m TESTONLY
  • You can also run the analysis on a tree as shown below:
    $ iqtree -s input.phy -m <model_name>
  • To re-run the analysis, use the following command:
    $ iqtree -s aligned_seqs.fasta -m <model_name> -redo

References

  1. S. Kalyaanamoorthy, B.Q. Minh, T.K.F. Wong, A. von Haeseler, L.S. Jermiin(2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods, 14:587-589.
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Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba
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