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When doing MLE with the R package ape or phangorn, is it possible to set the substitution model to Mk? If so, how does one do this?

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    $\begingroup$ I'm voting to close this question as off-topic because this belongs on Bioinformatics SE $\endgroup$ – The Last Word Jun 13 '18 at 18:26
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    $\begingroup$ SE Biology has an established question tag for bioinformatics, so that property alone should not be reason for closing the question as off-topic. $\endgroup$ – Namenlos Jun 13 '18 at 18:54
  • $\begingroup$ When u have a Stack Exchange website solely dedicated to bioinformatics work, I would suggest that you ask your question there. $\endgroup$ – The Last Word Jun 13 '18 at 18:55
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    $\begingroup$ I will do that. The existence of the Bioinformatics SE does not make this question off topic, however. $\endgroup$ – Namenlos Jun 13 '18 at 18:59
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From reading though the documentation, the Mk model does not appear available.

Although the JC69 model is, which this source describes as a slightly less generalized form as Mk. The JC69 model still assumes equal substitution rates and equal base frequencies. To use the JC69 model in phangorn set the model to "JC" and in ape set the model to "JC69".

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  • $\begingroup$ Of course this will not work if you have more than 4 discrete states - JC69 is a DNA model of sequence evolution. Look into using a program which isn't R. RAxML, IQ-TREE, MrBayes all allow Mk. $\endgroup$ – NatWH Jun 13 '18 at 19:44
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The R package diversitree has a large range of models including functions to optimise under Mk. Perhaps have a look at that.

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