Phylogeny Analysis tools

Question

[nazninislamnif]

I got a draft assembly genome of one kind fish. I have annoted the assembly by Maker and Interproscan. And now I want to do some evolution analysis, in particular, construct phylogeny tree for this genome and some other fishes' genomes released.

I tried MEGA to construct the phylogenetic tree but it failed cause the genome data is huge.

Could anyone recommend a tool or protocol for this phylogeny analysis? It will be very helpful if the tools web-based.

Thank you for sharing! Any suggestion, discussion or comment will be welcomed. :)

[Dunois]

Coming from your other post here:

I don't think you necessarily need to do anything else to infer a phylogenetic tree. You already have the species trees OrthoFinder has inferred--these can be found in the Species_Tree directory (there should be a primary tree, and some alternative configurations if any were found).

If you want to construct a tree with some other data (e.g., you wish to include other species in the tree), you could potentially use one (or all) of the single copy ortholog sets reported by OrthoFinder for this purpose.

[nazninislamnif]

Thank you.... I ran orthofinder as you suggested but I can't see the tree as Dendroscope is failed to install in my Utuntu. Any help?

[Dunois]

Just try and view the tree on iTOL? I gather that you have an installation of MEGA lying around. It should also be able to visualize the tree.