On 7 Oct 2019, at 2:19 am, Vincent Lynch <vincent...@gmail.com> wrote:Hi All,I'm using IQ-Tree to do ASR on a binary encoded morphological dataset and have some questions.1) ModelFinder indicates the best model is GTR2, but I cannot find an explanation of what this model is, is it described anywhere?.
2) My dataset includes missing data coded as "?", rather than skipping columns with ? IQ-Tree does the ASR on these sites. Is that normal?
3) The IQ-Tree ASR does get] it "right" most of the time when a column includes ? sites. Can it also predict whether a ? in an extant species is likely to be either 0 or 1? If so how can one access this data?
Thanks!Vinny--
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This is the general time reversible model for binary data (that’s why the suffix “2”). It’s the same merit as GTR for DNA, just adapted for 2 character states.
Good question. Right now there is no such option, as ASR is meant for (extinct) internal nodes. But why do you need such a feature? If there is a good reason why it’d be useful, then we will consider to implement that.
CheersMinh
Thanks!Vinny--
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