Is there a multiple sequence alignment that people use to construct phylogenetic trees in ugrad teaching labs with organisms that students relate to? Maybe some involving gene duplications? #molecularevolution #phylogenetics
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We get them to generate the multiple alignment by first retrieving BLAST hits then using MAFFT. The organisms aren't the kinds of things that students would relate to (i.e. Blastocystis, a human gut commensal). But there are gene duplicates in the data that they retrieve.
Fairly sure my UG course used primate 16s rDNA or mitochondrial genes to learn tools of the trade. And then once more sophisticated, re-analysis of viral genomes to track epidemiological spread via character evolution etc.
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