Command using SpeciesRax

[Yongze Yin]

Hi Benoit,

I am trying to infer a species tree inputting a set of unrooted gene trees using speciesRax. And I have two questions regarding the command I should use:

1. In the family file, I provided with both my unrooted gene tree and alignment(since it is mandatory) following the geneRax manuel. Is this the right thing to do?

2. I am using --si-strategy SKIP, but geneRax still asks me for an input species tree. Did I miss another "speciesRax" executable somewhere in the bin?

It will also be super helpful if there is an example command running speciesRax. Thank you for the software!!

Best,

Yongze

[Benoit Morel]

Hi Yongze,

1. You don't need the alignments for SpeciesRax. Even if you provide them, they won't be used because the SpeciesRax likelihood is computed from the gene trees only. This was indeed very unclear in the wiki.

2. There is no SpeciesRax executable. You need to use --si-strategy HYBRID to enable the species tree inference.

You are totally right about the examples, I will add several use-case examples this week, and work again on the wiki.

Thanks a lot for your questions, this will help me improving the documentation. If there is anything else, please do not hesitate.

Best,

Benoit

[Benoit Morel]

Hi Yongze,

I followed your good advice and started adding examples in the repository.

You can find a SpeciesRax example here: https://github.com/BenoitMorel/GeneRax/wiki/Examples#species-tree-inference-with-speciesrax

I hope it helps.

Best,

Benoit

[Yongze Yin]

Hi Benoit,

That is very helpful and the example is more than clear! Thank you!

Best,

Yongze