Question

explain how a scientist would use dna or protein sequences taken from three different organisms to construct a cladogram

Answer 1

@monsterprincess We align the sequences under formulas designed to adhere to our best understanding of evolution in molecular sequences. From that alignment (though sometimes we uses multiple alignments if they all are equally valid) we use tree building algorithms. The most common and most robust algorithms are maximum likelihood methods (a commonly used software package that implements this is RAxML) and Bayesian statistics that use multichain monte carlo markov processes (MCMC) to find the most likely tree (Mr. Bayes is a widely used Bayesian statistics program). I won't go into the serious math end of it unless you really want to.