User: BlastedBadger
BlastedBadger • 90
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Posts by BlastedBadger
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... I want to input an alignment (fasta format) for Beast2, but having to rewrite the entire data (8 million sites) into the XML file seems like a waste of space.
Does anyone know if there is a syntax that would allow inputting the alignment **from an external file**?
As an example, I have the followin ...
written 5 weeks ago by
BlastedBadger • 90
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... Ok, I managed to put up this basic syntax plugin: .
...
written 14 months ago by
BlastedBadger • 90
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... The programs from the PAML package by Ziheng Yang ([1997][1], [2004][2]) use a common input file format, containing parameters:
It's basically a list of `key = value`, and comments starts with an asterisk `*`:
Here is an short exerpt suited for the `codeml` program:
seqfile = myalignment.phy
...
written 14 months ago by
BlastedBadger • 90
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... The [bioconvert](https://github.com/bioconvert/bioconvert) project can also perform this particular conversion (among many other). ...
written 18 months ago by
BlastedBadger • 90
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... I created a gene distance matrix, based on GO terms similarity (using the R package `GOSemSim`).
I am then basically doing the following, where `gene_dist` is my distance matrix:
plot(hclust(gene_dist, method="average"))
I don't understand why the displayed tree from `plot.hclust` *is not ult ...
written 2.0 years ago by
BlastedBadger • 90
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... Yes thanks! I am not an expert, but here some of your data is categorical (ST, sex). For those, if you want to detect a correlation (for example ST versus sex), you should rather use `fitPagel` from the package `phytools` of Liam Revell. There is also the package `corHMM` from J. Beaulieu for more e ...
written 2.1 years ago by
BlastedBadger • 90
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... I understand from this [page](http://jul2018.archive.ensembl.org/info/genome/compara/species_trees.html) that that one is not the tree used in the protein trees pipeline. Also it is a fully resolved tree, and therefore compared to the NCBI topology makes some choices regarding uncertain branching or ...
written 2.1 years ago by
BlastedBadger • 90
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... Hello, could you please give more biological context? What are representing the tip of your phylogeny ? A sequence from an individual? Having some pathology? Why do you want to know which ST has the highest percent of males? Is it to identify sampling biases? Did you do an exhaustive sampling? Depen ...
written 2.1 years ago by
BlastedBadger • 90
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... Hi,
I have a problem specific to the EnsEMBL Compara database, which is how to retrieve the species tree that was used to run TreeBest in the Compara pipeline. I am basing this question on the [version 93](http://jul2018.archive.ensembl.org/info/about/speciestree.html).
# In short:
Does anyone kno ...
written 2.1 years ago by
BlastedBadger • 90
• updated
2.1 years ago by
Emily_Ensembl ♦ 21k
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... Alright, convertf from Eigentools is doing the same ...
written 3.4 years ago by
BlastedBadger • 90
Latest awards to BlastedBadger
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5 weeks ago,
created an answer that has been accepted.
For A: Syntax highlighting for PAML's control files in Vim
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5 weeks ago,
voted at least 25 times.
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
Popular Question
21 months ago,
created a question with more than 1,000 views.
For dN/dS in a tree (multiple genes)
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2.6 years ago,
created a question with more than 1,000 views.
For dN/dS in a tree (multiple genes)
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2.8 years ago,
created a question with more than 1,000 views.
For Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
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