Does alisim use internal node labels in input tree for output?

[nathanael....@gmail.com]

Hi guys,

I'm fairly sure it does, but just wanted to clarify before assuming: does alimsim use input node labels to label output sequences when specifying --write-all during alisim?

Many thanks for your help,

Nathanael

[Ly Trong Nhan]

Hi Nathanael,

Thank you for using AliSim!

I can confirm that you're right. When users specify '--write-all', AliSim uses the labels of internal nodes if they're specified in the input tree file. Otherwise, AliSim automatically generates the labels and outputs them in a new tree file *.full.treefile. 

Btw, please use the latest version for your simulations: https://github.com/iqtree/iqtree2/releases/tag/v2.2.2.7

Please feel free to contact us if you have any questions.

Cheers,

Nhan  

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