Noob phylogeny question

Hey all,

What genes would be good candidates for a BLAST in mammals (or others in animalia) for identity consideration?

So you mean as orthologs, or are you trying to identify organisms?

LIke @Mercer, i’m unsure what the question is trying to ask. What does “identity consideration” mean?

If the question is: which genes could be used to identify the species, that is not really a question about the phylogeny.

Sorry I was not articulate enough.

I wanted to compare sequence identity for a gene within a genus for a simplistic construction of a tree.

This may be a totally bad approach and/or not sure on how to find good candidate genes for various genuses.

Depends on the genus. A good candidate gene would be one that’s been well-sampled for the genus, and that would usually mean that it’s been sequenced for a phylogenetic study of that genus. I advise searching for those studies, which would lead you to the GenBank accession numbers. BLAST would be useful largely to find other taxa for which that gene had been sequenced. Of course if trees are what you’re looking for, any phylogenetic study you find should already have them.

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Thank you all as I now found what I was looking for!

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What did you find?

I looked at 3 cytb haplotypes for ursus that I found via your advice from this paper: Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture | Molecular Biology and Evolution | Oxford Academic (oup.com)

Definitely learned more (had already heard) the importance of rigour in comparisons.

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