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User: BlastedBadger

gravatar for BlastedBadger
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90
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Thule
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Posts by BlastedBadger

<prev • 21 results • page 1 of 3 • next >
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Input alignment for Beast as an external *link* in the XML control file.
... 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 ...
beastgen beauti beast beast2 written 5 weeks ago by BlastedBadger • 90
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Answer: A: Syntax highlighting for PAML's control files in Vim
... Ok, I managed to put up this basic syntax plugin: . ...
written 14 months ago by BlastedBadger • 90
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Syntax highlighting for PAML's control files in Vim
... 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 ...
vim paml written 14 months ago by BlastedBadger • 90
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Answer: A: Convert Nexus format to Newick format
... 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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Why is an hclust plot not ultrametric with "average" agglomeration method?
... 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 ...
R hierarchical clustering written 2.0 years ago by BlastedBadger • 90
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Comment: C: Stratify phylogeny based on variables - e.g. which ST are represented by high %
... 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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Comment: C: Extract species tree from the Ensembl Compara database
... 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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Comment: C: Stratify phylogeny based on variables - e.g. which ST are represented by high %
... 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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Extract species tree from the Ensembl Compara database
... 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 ...
ensembl database tree written 2.1 years ago by BlastedBadger • 90 • updated 2.1 years ago by Emily_Ensembl ♦ 21k
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Comment: C: Convert SNP dataset from PACKEDANCESTRYMAP to plink (PED)
... Alright, convertf from Eigentools is doing the same ...
written 3.4 years ago by BlastedBadger • 90

Latest awards to BlastedBadger

Scholar 5 weeks ago, created an answer that has been accepted. For A: Syntax highlighting for PAML's control files in Vim
Supporter 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)
Popular Question 2.6 years ago, created a question with more than 1,000 views. For dN/dS in a tree (multiple genes)
Popular Question 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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