User: BlastedBadger
BlastedBadger • 50
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Posts by BlastedBadger
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... Alright, convertf from Eigentools is doing the same ...
written 7 months ago by
BlastedBadger • 50
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... The convertf from AdmixTools is really not working as it should. For example, the `.fam` file produced by using "PACKEDPED" output does not contain any population information anymore. The first column (family IDs) is just a row number... I am gonna try with Eigensoft. ...
written 7 months ago by
BlastedBadger • 50
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... I have downloaded the "Affymetrix Human Origins Curated" dataset from [David's Reich Lab][1], but am totally at loss to understand which format it is, and how I could convert it to something usable by `plink`
So far, I have downloaded the utility `convertf`, from the [AdmixTools][2] package for exa ...
written 7 months ago by
BlastedBadger • 50
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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 11 months 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 11 months 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 11 months 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 11 months ago by
BlastedBadger • 50
• updated
11 months ago by
Michael Dondrup ♦ 44k
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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 13 months 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 14 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 18 months ago by
BlastedBadger • 50
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