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A user should be able to convert a search for genes into a search for orthologs of a result set. This can be done by faceting on the epl_gene_tree field and then rewriting the query as a disjunction o…
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Hi,
thank you for your interesting package. In my dataset of ~20,000 cells and 26,897 genes, I found that the tool found 20,000 unique significant genes. I wanted to ask whether this makes sen…
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Hello Sergei,
I'm not sure what's going on, but when I run the same inputs on my computer vs. a cluster with CPU=10 parameter set, I get different results for this gene. Attached herein are the 2 d…
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Hi!
I'm performing maximum likelihood branch length estimation following PhangornTreeBuildingWalkthrough, however I get
estimatePhangornTreeAll(alndir="genes/", treefile="constr.tre", output.fil…
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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…
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The gene family detail component is using esoteric knowledge of the Legume Information System to create links to gene family trees (though the URL is provided via the config file, the GET structure of…
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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…
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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.
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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…
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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…