Phylogenetics analysis between diverse species

Question

[dimitrischat]

Hello all,

Hope everyone is well.

So i was appointed with a task, and i need some guidance. Attention, the one that gave me the task may not have explained this very clearly. I will write what he exactly asked of me, and what he gave me as primary data.

So he gave me 4 bed files (human genome) with chr and coordinates(start/stop), and asked me to do: "sequencing/coordinates conservation between diverse species".

Is that doable with coordinates only or do i need sequences in fasta format (phast uses fasta format)? I just dont understand how i will find "conservation between diverse species" only with coordinates. It seems weird to me.

I have found these programs: TargetOrtho2, Phast and BUSCO(?). Are they any good? Should i continue with one of them that you may have experience with?

Thanks

[Michael]

I think he wants you to find the precomputed sequence conservation from some database, genome browser, it is perfectly doable with the input you got, Is this an assignment?

[dimitrischat]

Thanks for the answer. Yes its an assignment. How should i proceed ?

[dimitrischat]

Hello. Any input? Thanks

[Michael]

Did you look at UCSC genome browser and the conservation track there? I think it is all pre-computed and much easier to get than you thought.

[GenoMax]

If all the data you have is human what diverse species are you referring to?

[dimitrischat]

Yes its all human. He didnt clarify, but i am guessing species that represent different taxonomies (or some significant sub category).