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using complex models for topology tests #255

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faylward opened this issue Jan 3, 2024 · 0 comments
Open

using complex models for topology tests #255

faylward opened this issue Jan 3, 2024 · 0 comments

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@faylward
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faylward commented Jan 3, 2024

Greetings - for testing the likelihood of a constrained tree compared to a reference (IQ-TREE Advanced Tutorial section "Tree topology tests"), is there a way to specify a complex model with -m ? The current example in the manual is something like "iqtree -s example.phy -z example.treels -m GTR+G". I am currently using a reference tree that was made with a complex model, and I was wondering if it was possible/meaningful to use a C60 model for this step.
Also, could you clarify the effect of using multiple iterations with the -n flag for this step? I am hoping to increase the sensitivity of my topology comparisons, so any tips you have for tweaking the parameters here would be welcome.
Thank you,

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