What are the differences between the user-provided tree file and the ".treefile", generated from an ASR job?

[Gabriel DUPRE]

Hi,

I am doing ancestral sequence reconstructions (ASR), and I have a question about some output files.

I am launching the ASR analysis by specifying the best-fit substitution model and my consensus tree in my command line. After the job was done, a ".treefile" is generated, in which node labels were automatically added for every internal node.

Is this ".treefile" the same tree as mine, with internal node labels added?

Can this "treefile" differ to my consensus tree in terms of genetic distances between nodes and topology?

I am not sure how this ".treefile" was built. Can I have more information about its construction?

Best regards

Gabriel

[Minh Bui]

Hi Gabriel,

On 12 Jun 2020, at 6:42 pm, Gabriel DUPRE <gabriel...@gmail.com> wrote:

Hi,

I am doing ancestral sequence reconstructions (ASR), and I have a question about some output files.

I am launching the ASR analysis by specifying the best-fit substitution model and my consensus tree in my command line. After the job was done, a ".treefile" is generated, in which node labels were automatically added for every internal node.

Is this ".treefile" the same tree as mine, with internal node labels added?

Depends on whether you fixes the topology of the starting tree or not. What is the command line? If you use “-t” option then IQ-TREE uses the input tree as starting tree and will further optimise it. With “-te” option, it will fix the tree topology.

Can this "treefile" differ to my consensus tree in terms of genetic distances between nodes and topology?

See above

I am not sure how this ".treefile" was built. Can I have more information about its construction?

I assume this is a general question about IQ-TREE algorithm. If so, have a look at our paper: https://doi.org/10.1093/molbev/msu300

Minh

Best regards

Gabriel

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