User: BlastedBadger
BlastedBadger • 50
- Reputation:
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- Location:
- Thule
- Last seen:
- 6 days, 18 hours ago
- Joined:
- 1 year, 5 months ago
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- y***@hotmail.fr
Posts by BlastedBadger
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... 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
BlastedBadger • 50
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... 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 ...
written 6 days ago by
BlastedBadger • 50
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... 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
BlastedBadger • 50
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... 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 ...
written 25 days ago by
BlastedBadger • 50
• updated
24 days ago by
Michael Dondrup ♦ 42k
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... 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
BlastedBadger • 50
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... 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 ...
written 3 months ago by
BlastedBadger • 50
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... 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
BlastedBadger • 50
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... 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), ...
written 7 months ago by
BlastedBadger • 50
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... 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 ...
written 12 months ago by
BlastedBadger • 50
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