Phylogeny Study Based On Whole Genome Sequences

Question

[GAO Yang]

Hi, everyone~

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

I know the protein sequences will be needed. So, the protein sequences were predicted , then aligned with NCBI database; sequences without hit were removed. Other fishes' pro can be downloaded easily.

Could anyone recommend a tool or protocol for this phylogeny analysis? Doesn't matter whether win or Linux, web-based or local.

In addition, I found this CVTree which seems pretty user-friendly. But the built-in database contains no fish data. I need to upload them, so I tried to upload the pro sequences, one file for each species. The results return with empty files. it seems don't support the analysis for the uploaded multi-files, multi-species data?

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

Answer 1

[Josh Herr]

This same question is posted every couple of months... See here, here, and here for the last few months alone.

I perhaps can see a whole genome phylogeny of a bacterial genome, but why would you want to do a whole genome phylogeny of a eukaryote (also a fish with a fairly large genome)? Have you attempted a phylogeny with a single or suite of genes and this was not robust enough?

Why do you say protein sequences will be needed? Yes, you can construct a phylogenetic tree with protein data, but this is inferred from your genome sequence, so why not just use the genome sequence?

Why do you want to construct a whole genome phylogeny? Have you thought about why you want to do this? What is your research question?

[GAO Yang]

Yeah, you are right~ protein won't be necessary. I decide to do this with some conserved genes/proteins. And thank you for your link and question, really good guide for newbie.