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Currently the "edge data.frames" are built to work with the geom_line() geom. However, using geom_segment() might give more flexibility. In particular it would open the way to use geom_link(), geom_be…
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Hi there,
Just curious what your thoughts are (and from others) about the threshold we use to collapse the boostrap support values for each gene tree prior to the PhyParts visualisation.
In your…
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Hi,
I am trying to visualize gene trees inferred with RAXML. I have no problems with other set of gene trees from IQTREE, but with RAXML trees I found a first message: "The tree set possibly contains…
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This may have already been addressed--Steven was re-calculating gene families recently. If you have a gene from lupine you won't find it in the family tree display despite linking out from the appropr…
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Hi,
I used RERconverge to run more than 1 million genes (non-coding regions), but it runs too slowly. so I want to split the gene file (with branch length estimated by paml baseml) to multiple …
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Hi,
I have run OrthoFinder with 4 genomes belonging to the same species and I would like to know how many of the single copy gene trees have the same topology as the species tree. Is something that…
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Hello!
I'm running into an issue when I try to run RERconverge with my data.
When I use the function of readTrees , It will prompt me with the following information:
>toyTrees=readTrees("TreeFile.t…
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Hi Sir,
Thank you very much for this package!
I recently bumped into a difficulty in gene tree simulation using Phybase.
It failed to simulate gene trees for the third tree in the file but it …
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I am trying to associate a binary phenotype with RERs. I have a master tree with 232 species and 1680 gene trees. I tested the code below with 100 species and it works, but when I try all the genes It…
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Hello David,
I encountered the following issue while running OrthoFinder: "ERROR: Species tree inference failed."
The command I used is: orthofinder -f ./data -t 24 -a 10 -M msa -S diamond -A m…