tag:blogger.com,1999:blog-8386055846297828307.post5435753189099005929..comments2024-03-28T07:34:49.133+01:00Comments on The Genealogical World of Phylogenetic Networks: Trivial data, but not so trivial graphsUnknownnoreply@blogger.comBlogger2125tag:blogger.com,1999:blog-8386055846297828307.post-13402603357100249042018-09-06T11:39:13.763+02:002018-09-06T11:39:13.763+02:00Dear Damian,
I still like the "commagram&qu...Dear Damian, <br /><br />I still like the "commagram" (even though it's a phylogenetic tree, there are no reticulations), but the main problem (I can't judge the maths) with your method is <br />a) that it's published in the Ukrainian Botanical Journal (so I suppose the number of people picking it up will be quite limited), and <br />b) that it doesn't come with a programme/script (as far as I can see) doing the Bayesian weighting and inferring the so-optimised tree that includes likely and theoretical ancestors.<br /><br />In order to have people play around with it, you could upload the NEXUS files you used for PAUP*, a walk-through, as well as the graphics on an open repository, e.g. <i>figshare</i> or maybe, in this particular case, <a href="https://paleorxiv.github.io/" rel="nofollow"><i>PaleorXiv</i></a>. You have a similar problem here as Zander had/has (I always liked his papers, like <a href="https://researchinpeace.blogspot.com/2017/09/two-papers-you-may-want-to-read-before.html" rel="nofollow">this one</a>) with his ideas. Providing a theoretical-philosophical piece for a practical thing that could interest mainly practioners with no/little mathematical background whatsoever: palaeontologists.<br /><br />This is why everyone uses the post-analysis weighting method implemented in the WHS-supported TNT to get some resolved tree in palaeonotlogy, despite many ancestor-descendant and other signal issues in their data. Because it's just pressing buttons these days.<br /><br />Cheers, GuidoDas Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-8386055846297828307.post-18243046337646397912018-09-03T17:26:28.958+02:002018-09-03T17:26:28.958+02:00For those readers not familiar with networks, I pr...For those readers not familiar with networks, I proposed a parsimony-based tree-based method for infering ancestor-descendant relationships : http://ukrbotj.co.ua/archive/74/2/103<br /><br />As you said, "we need tree inferences that can optimize an older taxon on an internal branch or node, to accommodate potentially ancestral forms", this is exactly what my algorithm is doing.Anonymoushttps://www.blogger.com/profile/17724042372602455356noreply@blogger.com