User: BlastedBadger

gravatar for BlastedBadger
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Thule
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6 days, 18 hours ago
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1 year, 5 months ago
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Posts by BlastedBadger

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Where has the R Ape 'chronogram' function gone (Non-Parametric Rate Smoothing)?
... From [Ape's log][1], `chronogram` has indeed been deprecated. > CHANGES IN APE VERSION 2.5-2 > > DEPRECATED & DEFUNCT > > o evolve.phylo() and plot.ancestral() have been removed. > > o chronogram(), ratogram(), and NPRS.criterion() have been removed. But as ment ...
written 6 days ago by BlastedBadger50
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Where has the R Ape 'chronogram' function gone (Non-Parametric Rate Smoothing)?
... Hi, I want to use several methods to estimate the age of nodes in a phylogeny. I plan on using Ape's `chronos` function that relies on a penalized likelihood method ([Sanderson 2002][1]), but I also would like to test the NPRS method (Non Parametric Rate Smoothing, [Sanderson 1997][2]). I read som ...
R chronogram nprs phylogenetic dating ape written 6 days ago by BlastedBadger50
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Comment: C: UPGMA method when tree leaves have different known ages
... I am using gene trees from Ensembl, that I cut at family level. So for example, I have around 15000 trees for Rodentia. They can have from 5 to 50 leaves (most of them between 5 and 10 I guess, but I didn't check). Yes BEAST would be the canonical tool for age inference I suppose, I need to get to k ...
written 24 days ago by BlastedBadger50
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UPGMA method when tree leaves have different known ages
... Hi, I have gene trees, with molecular distances. In these gene trees, I have speciation nodes, whose absolute age is known. I also have *gene duplication* nodes, whose absolute age is *unknown*. These molecular trees are highly not ultrametric (meaning there isn't the same distance between leaf an ...
phylogeny upgma molecular clock time-tree dating written 25 days ago by BlastedBadger50 • updated 24 days ago by Michael Dondrup42k
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Answer: A: Inconsistent query coordinates between chain and net alignments in UCSC
... Aaah, alright, I got the answer asking the UCSC genome browser mailing list [here][1]: this is actually specified in the doc that query coordinates in chain are relative to the reverse-complemented sequence when the strand is "-". Same for axt. [1]: https://groups.google.com/a/soe.ucsc.edu/d/msg/ge ...
written 11 weeks ago by BlastedBadger50
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Inconsistent query coordinates between chain and net alignments in UCSC
... I am searching for a gene in the *rock hyrax* genome (`proCap1`) using the *mouse* ortholog, which is located in `mm10` at chr17:71344493-71475343. Using the UCSC mysql database, I don't get the same coordinates in proCap1, depending on whether I search in the "chain" or the "net" alignment. Once ...
alignment net chain ucsc written 3 months ago by BlastedBadger50
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Comment: C: Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
... oops, after reading more on the subject on Biostars, I realized that my codeml run was never properly finishing! It gives an error like `Species ENSGT00790000122969.a?` that I need to fix first. Will come back when it's done... ...
written 7 months ago by BlastedBadger50
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Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
... Hi, I am trying to estimate divergence times (of genes) in a gene tree, using dS (synonymous substitution rates). At least I am trying to map substitution numbers to branches, then if it corresponds to time is another question. I am using complete gene trees from Ensembl (one gene tree at a time), ...
phylogeny substitution rates paml ds codeml written 7 months ago by BlastedBadger50
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dN/dS in a tree (multiple genes)
... Hi, this is kind of an emergency, since I have to handle my MSc internship report in one week and there is an analysis that would be a very nice addition to it. ## What I need ## I am using the [Ensembl](http://www.ensembl.org/) database, and want to know which branches in the gene trees are sub ...
kaks dn/ds phylogenetics paml dnds written 12 months ago by BlastedBadger50

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