User: BlastedBadger

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Posts by BlastedBadger

<prev • 18 results • page 1 of 2 • next >
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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 29 days ago by BlastedBadger70
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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 6 months ago by BlastedBadger70
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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 7 months ago by BlastedBadger70
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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 7 months ago by BlastedBadger70
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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 7 months ago by BlastedBadger70
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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 7 months ago by BlastedBadger70 • updated 7 months ago by Emily_Ensembl19k
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Comment: C: Convert SNP dataset from PACKEDANCESTRYMAP to plink (PED)
... Alright, convertf from Eigentools is doing the same ...
written 23 months ago by BlastedBadger70
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Comment: C: Convert SNP dataset from PACKEDANCESTRYMAP to plink (PED)
... 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 23 months ago by BlastedBadger70
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Convert SNP dataset from PACKEDANCESTRYMAP to plink (PED)
... 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 ...
plink snp written 23 months ago by BlastedBadger70
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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 2.3 years ago by BlastedBadger70

Latest awards to BlastedBadger

Popular Question 4 months ago, created a question with more than 1,000 views. For dN/dS in a tree (multiple genes)
Popular Question 14 months ago, created a question with more than 1,000 views. For dN/dS in a tree (multiple genes)
Popular Question 17 months 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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