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Questions - phylogeny

Cannot import name 'TextFace' error while using ETE3 for Phylogeny Tree

I am trying to install ETE3 for phylogeny analysis but while installing it is showing error:cannot import name 'TextFace' I tried all the available options but could not succeed. Any help will be appr...
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shivam

python

bioinformatics

fasta

phylogeny

ete3

Votes: 0

Answers: 0

Phylo correlogram in R bootstrapping error?

I am trying to create a phylo correlogram based on my data using phyloCorrelogram from the phylosignal package in order to test for presence of a phylogenetic signal. My data is in the so-called phylo...
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Geomicro

r

phylogeny

ape-phylo

Votes: 0

Answers: 1

Latest Answer

You have no data associated to your tree. Your tree is a phylo4d object which has the "tree" information but no data attached to it. You need something like that library(phylobase) g1 <- ...
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Thor6

Rename phylo tip labels with separate df

I am looking to rename 1290 tip labels in my phylo tree using a second df. I am able to rename one label at a time using the below code: phylo$tip.label[phylo$tip.label=="e54924083c02bd088c69537...
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Geomicro

r

tree

phylogeny

Votes: 0

Answers: 2

Latest Answer

You can use the value matching function %in% to first detect which labels are in the "old labels" column in your data frame and then replace them by the "new labels". ## A random t...
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Thomas Guillerme

Phylo tree has no branch lengths using phylosig () R

I am having a hard time understanding why my phylo tree (imported as a phyloseq object from QIIME2) appears to have no branch lengths when used in phylosig(). I am trying to compute the phylogenetic s...
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Geomicro

r

phylogeny

phyloseq

Votes: 0

Answers: 1

Latest Answer

The problem is not the lack of branch lengths in the tree. What the error message is saying is that the tree does not have the tips that correspond to the names of values in the trait variable. glacia...
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nya

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