-
Hi!
I'm performing maximum likelihood branch length estimation following PhangornTreeBuildingWalkthrough, however I get
estimatePhangornTreeAll(alndir="genes/", treefile="constr.tre", output.fil…
-
If not all gene trees have sequences for all species, for each such species a single empty sequence could be added to the alignment, and thus the gene tree, to create a valid *BEAST analysis.
-
Hello. This is part of the message provided by the program. I have tried many thinks but nothing appears to work when I want to analyze nt. The aa analysis runs properly. Your comments will be appreci…
-
I used the "tree" option with backbone.nwk and the alignments of 12 genes including 2538 species. I always got error message "In cluster species/output/udance/3, 1 gene tree(s) with lower than 0.80 me…
-
Currently, I have the following setup:
`gene_tree = read(gene_tree_fp, format='newick', into=TreeNode)`
I would like to return the Newick string representation of the gene_tree but without the dista…
-
Hello,
I was wondering if this is possible to use shoot with existing database of multiple alignment and trees.
Let's say that I reproduce the same directories as orthofinder and include diamond d…
-
Hi Thorsten
Thank you so much for this handy tool. I was wondering if there is a possibility to also save the (concatenated) sequences of the identified MLST genes to file? Similarly to the novel a…
-
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…
-
Hi,
When testing -M msa -T fasttree, raxml, raxml-ng, and iqtree with -f ExampleData using OrthoFinder 2.5.5, I find that raxml fails, while the other ML codes work. The failure occurs near the end…
-
**Describe the bug & to reproduce**
When running `-t 16` or `-t 32`, ASTRAL appears to complete but `freqQuad.csv` is completely empty. The only error reported is:
```
Final quartet score is: won…