https://problog.stephentpollard.com/enContents © 2022 <a href="mailto:public@stephentpollard.com">Stephen Pollard</a> Tue, 04 Jan 2022 20:50:19 GMTNikola (getnikola.com)http://blogs.law.harvard.edu/tech/rsshttps://problog.stephentpollard.com/posts/cdmcmc/Stephen Pollard<div><p>2015-2017</p> <p>The Convergence-Divergence MCMC is a Markov chain Monte Carlo method used to fit a customized model of the expected distribution of the convergence, divergence, and distance between many different branches on a phylogenetic tree. The definition of a convergence between two branches is when there are two substitutions at the same site on the two branches to the same amino acid. For example, a substitution on branch #403 at site 14 from Alanine to Glutamine and a substitution on branch #586 at site 14 from Methionine to Glutamine would be a single convergence event between branches #403 and #586. If either of the substitutions above were to an amino acid other than Glutamine, the event would count as a divergence. The distance between the branches on a phylogenetic tree is calculated from the top (ancestor) of one branch, back in time to the most recent common ancestor, and down the top (ancestor) of the other branch.</p> <p><a href="https://problog.stephentpollard.com/posts/cdmcmc/">Read more…</a> (1 min remaining to read)</p></div>PerlPhylogeneticshttps://problog.stephentpollard.com/posts/cdmcmc/Thu, 28 Nov 2019 07:00:00 GMThttps://problog.stephentpollard.com/posts/perlmodules/Stephen Pollard<p>2012-2019</p> <p>A collection of Perl modules for phylogenetic analysis and statistical inference.</p> <p>Repository: <a class="reference external" href="https://publichg.stephentpollard.com/PerlModules">https://publichg.stephentpollard.com/PerlModules</a></p>PerlPhylogeneticshttps://problog.stephentpollard.com/posts/perlmodules/Thu, 28 Nov 2019 07:00:00 GMT