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The current version of phyloglmm cannot handle phylogenetic trees with polytomies. It will only take full phylogenetic trees (i.e., n tips, n-1 nodes, and 2(n-1) branches).
wzmli updated
5 years ago
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Hello,
Thank you for developing this program! I'm currently struggling to plot the results of an A00 analysis, with nodes converted to real time based on a pedigree mutation rate. I see that there …
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Currently, PhyloNext accepts phylogenetic trees in Newick format (due to its simplicity and widespread use).
However, our pipeline internally converts these Newick trees into Nexus format at one of t…
vmikk updated
5 months ago
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#### Description
We are currently using chewBBACA for genomic surveillance, and one of our workflows involves running the `JoinProfiles` function to add new samples to the results of historic sampl…
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Hello, I run the gt mode, and I met an error that two trees do not have the same topology, which means that phylogenetic tree from my mod file and the tree in coalescent unit from astral-species-tree.…
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Hi everyone,
I was using GTDB-Tk/2.3.2, and after updating to GTDB-Tk/2.4.0, some Spirochaetota bacterial species started clustering far from each other in the phylogenetic tree (shown in dark gree…
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Hello,
I'm doing a class project for undergrads where they collect morphological data on plants and use phangorn to create phylogenetic trees from their matrix of data. I decided for ease of data c…
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Hi prof Liu,
When I run mp-est, it comes out this error.
mpest control
Maximum Pseudo-likelihood Estimation of Species Trees (MPEST_1.5)
by…
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Hello, I am fairly happy to use TreeViewer as a tool of editing and
visualizing my phylogenetic trees. However, I am wondering how to rotate the tree at some nodes in TreeViewer just as Figtree do…
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A user recently sent me a tree and was astounded by what he is seeing in PATRIC, so I had to tell him that I always take the newick file and visualize the tree in FigTree due to this problem, but its …