Question: How to make a phylogenetic tree set in ASTRAL?
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gravatar for M.O.L.S
5 months ago by
M.O.L.S10
M.O.L.S10 wrote:

How do I create a tree set in ASTRAL from several files?

There are files for exons, introns and chromosomes.

There are different data types are represented.

There are a few loci are there for each datatype.

phylogeny • 221 views
ADD COMMENTlink written 5 months ago by M.O.L.S10
2

I think you will need to be more specific about your data and your goals.

ASTRAL takes gene trees as input and uses these to estimate a species tree under the multi-species coalescent model (or at least a heuristic approximation). Therefore, to run ASTRAL, you would need to first infer phylogenies for each of your orthologous gene sequence alignments.

Do you have those alignments and/or gene trees? Have you looked through the ASTRAL documentation?

ADD REPLYlink written 5 months ago by Dave Carlson320
1

If you know about ASTRAL, you presumably know why you'd like to use it as opposed to any other phylogenetic estimation approach. I'd recommend breaking your question up into multiple or search Biostars for some direction in introductory molecular phylogenetics. You can expect to have a different workflow for estimating the gene trees from each of the data sources you provided before getting to the ASTRAL stage.

ADD REPLYlink written 5 months ago by Brice Sarver3.5k

I don't know any other phylogenetic estimation approaches (programs?), apart from ASTRAL.

ADD REPLYlink modified 5 months ago • written 5 months ago by M.O.L.S10
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