tag:blogger.com,1999:blog-3342041114052632712.comments2024-01-20T16:39:42.179+11:00PhyloBotanistAlex SLhttp://www.blogger.com/profile/00801894164903608204noreply@blogger.comBlogger557125tag:blogger.com,1999:blog-3342041114052632712.post-19626310041181836242018-05-24T03:19:56.158+10:002018-05-24T03:19:56.158+10:00This comment has been removed by the author.Anonymoushttps://www.blogger.com/profile/14202016669712149094noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-2076173452196587262018-05-18T21:13:13.573+10:002018-05-18T21:13:13.573+10:00Hi,
i found that adding your libraries like "...Hi,<br />i found that adding your libraries like "export LD_PRELOAD='location of libraries separated by spaces'" before running faststructure fixes the problem with missing libraries.Anonymoushttps://www.blogger.com/profile/07521932199995318052noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-49608579652431128942018-05-01T07:47:11.903+10:002018-05-01T07:47:11.903+10:00It has been some time, but if memory serves I simp...It has been some time, but if memory serves I simply used Excel or LibreOffice Calc to make the graphs and then edited them in Inkscape.Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-31980744105458937952018-05-01T03:45:51.070+10:002018-05-01T03:45:51.070+10:00Hey Alex,
What program did you use to create the...Hey Alex, <br /><br />What program did you use to create the plot for the market share?<br /><br />Thanks!Anonymoushttps://www.blogger.com/profile/04315571004834515811noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-5717344606365388582018-04-25T02:41:34.273+10:002018-04-25T02:41:34.273+10:00Thanks for the shout-out regarding paleotree, and ...Thanks for the shout-out regarding paleotree, and even bringing up the topic of dating paleo-phylogenies at all. That said, I'm pushing people away from the simple algorithms (like what is possible in paleotree) and toward doing tip-dating in MrBayes or BEAST2, even with an empty character matrix. I think the node.dating function in ape is something like a maximum-likelihood tip-dating method, although I haven't played around with it yet.dwbapsthttps://github.com/dwbapst/paleotreenoreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-54653898048168017702018-04-11T07:56:51.155+10:002018-04-11T07:56:51.155+10:00Hm. I just reread the Vox piece that Harris found ...Hm. I just reread the Vox piece that Harris found unfair, and I am not sure I can even see where he is characterised as racist. The authors go out of their way to characterise him as a critical thinker who may have overlooked how weak Murray's case is. In fact they argue a lot of the same things about how one needs to freely and objectively discuss the science that Harris argued.Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-12335532089572400022018-04-11T07:37:10.453+10:002018-04-11T07:37:10.453+10:00This comment has been removed by the author.Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-33472918102632693602018-04-11T04:34:35.309+10:002018-04-11T04:34:35.309+10:00>But his otherwise reasonable points are comple...>But his otherwise reasonable points are completely overshadowed by his tendency to make it all about how mean his critics are to him for calling him biased<br /><br />We all have bias. That's not waht Harris complained about. He complained about being characterized as racist. But for you to downplay such a crucial and obvious aspect of this argument, suggests some strong bias on your behalf. To the extent that I'm inclined to interpret most of what you you write after that as largely the byproduct of misinformation. Jeff Huddlehttps://www.blogger.com/profile/06363054017025538659noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-3218300512295082012018-04-04T07:51:13.740+10:002018-04-04T07:51:13.740+10:00Yes, that is the only argument against phylogeneti...Yes, that is the only argument against phylogenetic systematics that makes some kind of sense. It could be said, however, that the idea of classifying all species into all supraspecific ranks was the result of Linnaeus not knowing about common descent, and that maybe we should change our approach to classification to match reality instead of insisting on a pre-theory of evolution approach while ignoring reality.Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-85705731410174063622018-04-03T18:58:45.271+10:002018-04-03T18:58:45.271+10:00Sister genera A1 and A2 are in Family A. The most ...Sister genera A1 and A2 are in Family A. The most recent common ancestral species of A1 and A2 is necessarily in either genus A1, genus A2, or some other genus. If the ancestor is placed in A1, then A1 is paraphyletic with respect to A2. If placed in A2, A2 is paraphyletic. If a third genus is invoked, that genus is paraphyletic with respect to A1 and A2. Strict monophyly in classification requires unclassified, unknown ancestors. Although practically we will never be able to know enough about most such ancestors, this seems inappropriate for an evolutionary science.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-51299793192078278852018-03-30T02:31:37.128+11:002018-03-30T02:31:37.128+11:00I found this very helpful, and have included the p...I found this very helpful, and have included the phrase "critical reading" in thanking reviewers. It is an important, and often thankless, task to review manuscripts. Thank you! hmusgrovehttps://www.blogger.com/profile/12554697084377688964noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-47261610124164573312018-01-26T09:40:18.369+11:002018-01-26T09:40:18.369+11:00How do I make one?How do I make one?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-74686491968706902542017-11-08T21:27:17.898+11:002017-11-08T21:27:17.898+11:00I just ran a quick SVD analysis on 4a158 and get t...I just ran a quick SVD analysis on 4a158 and get the bootstrap values on the resulting tree using your savetrees command, only they appear to be saved as branch lengths. Have you tried adding the parameter savebootp=nodelabels?Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-57921926787164506242017-11-08T17:31:17.331+11:002017-11-08T17:31:17.331+11:00Great post. I just ran svd quartet analysis with P...Great post. I just ran svd quartet analysis with PAUP like you did in linux. However, the final tree does not have bootstrap values with it.<br /><br />this is my command line at the end of the nexus file. Did you have this issue?<br /><br />begin paup;<br /> log file=svd.txt;<br /> lset nthreads=3;<br /> SVDQuartets evalQuartets=random speciesTree=yes partition=gabriel_data bootstrap=standard nreps=10000 ambigs=distribute treeFile=svd.tre;<br /> savetrees file=svd_boot.tre from=1 to=1 maxdecimals=2;<br /> log stop;<br /> quit;<br />end;<br /><br />gdvalehttps://www.blogger.com/profile/10724510767610610006noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-79122159781534397552017-10-29T17:22:29.210+11:002017-10-29T17:22:29.210+11:00Unfortunately I have no idea, not being a zoologis...Unfortunately I have no idea, not being a zoologist myself. Sorry.Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-42272194853746568482017-10-29T16:06:58.253+11:002017-10-29T16:06:58.253+11:00What species is the green crab? We saw thousands ...What species is the green crab? We saw thousands of them today amongst the mangroves on the Bobbin Head Boardwalk, in the Ku-Ring-Gai National Park, accessible from Bobbin Head Road, North Turramurra. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-75306447223554534432017-10-16T10:54:59.117+11:002017-10-16T10:54:59.117+11:00The well of garbage postmodernism is infinitely de...The well of garbage postmodernism is infinitely deephuwnoreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-9537839175868529372017-10-14T05:21:51.998+11:002017-10-14T05:21:51.998+11:00Clear, succinct explanation. Thanks!Clear, succinct explanation. Thanks!Ben Montgomeryhttps://www.blogger.com/profile/00139096146792116429noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-69383730623275811522017-09-18T19:33:58.383+10:002017-09-18T19:33:58.383+10:00Excelente Post! Felicitaciones!
(Esteban Meza)Excelente Post! Felicitaciones!<br />(Esteban Meza)Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-31856427834591726292017-09-02T00:15:14.478+10:002017-09-02T00:15:14.478+10:00Did you give a try to http://www.atgc-montpellier....Did you give a try to http://www.atgc-montpellier.fr/compphy/ ? all Online tool developped in my team.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-27179950311511501902017-08-26T15:59:54.440+10:002017-08-26T15:59:54.440+10:00Nice article and want share a tool for XML https:/...Nice article and want share a tool for XML https://jsonformatter.org/xml-formatterAwesomehttps://www.blogger.com/profile/15037598698637581441noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-72441173135066398982017-08-21T07:57:03.448+10:002017-08-21T07:57:03.448+10:00I can only speculate at the moment, but if they ha...I can only speculate at the moment, but if they haven't changed anything since I used it chooseK is really quite simplistic, merely selecting the highest likelihood score. But that is not how one usually does it, one would expect a saturation curve and choose the K where it flattens, even if an insignificantly higher value is at a higher K. (And then there is the possibility that there are two maxima, if you have a nested structure such as two groups of populations or suchlike.)<br /><br />Anyway, I can easily imagine that a slightly different seed will produce slightly different solutions, and if they are very nearly identical but differ in the exact likelihood values on the plateau then chooseK as I observed it then would pick whatever happens to be highest on that plateau. But again, speculation.Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-10727362844159393252017-08-21T03:35:16.169+10:002017-08-21T03:35:16.169+10:00Hello Alex,
I am also a new fastSTRUCTURE (=fs for...Hello Alex,<br />I am also a new fastSTRUCTURE (=fs for simplicity) user and hope you still review this part of your forum.<br />I have also faced with something strange in my fs results. I have run multiple fs runs (python faststructure.py) with different seed-sets. But, when I run chooseK.py to get an estimation number of subpopulations in my data set I get different outputs. This means that everything is identical in my faststructure.py script expect of seed-sets and I wonder why I get different K estimation.....!<br />for instance in one of my runs I get this<br />Running on 5 cores.<br />Starting fastSTRUCTURE at: Mon Aug 14 14:00:49 PDT 2017<br />Model complexity that maximizes marginal likelihood = 1<br />Model components used to explain structure in data = 10<br /><br /><br />and in the other run I get <br />Model complexity that maximizes marginal likelihood = 1<br />Model components used to explain structure in data = 7Anonymoushttps://www.blogger.com/profile/10703757585206338396noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-63336600673456869932017-08-03T00:49:20.409+10:002017-08-03T00:49:20.409+10:00Very nice. When I use one root calibration I get a...Very nice. When I use one root calibration I get a tree with that root age, but when I use the root and several other calibration points I get a tree with ages older than the maximum ages.cbuddenhagenhttps://www.blogger.com/profile/12740386663793698087noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-66214147722298918712017-07-19T08:29:21.111+10:002017-07-19T08:29:21.111+10:00Very nice example. Philosophy is easy to do badly...Very nice example. Philosophy is easy to do badly, even for brilliant people, and very hard to avoid doing at all.Paul Torekhttps://www.blogger.com/profile/13947970013402114431noreply@blogger.com