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I'm a beginner in bioinformatics and forgive me for having some questions that look stupid.
The first question is about the input file requirements. Where can I get the gene tree with values for br…
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@josephwb has a supertree study with >1000 trees.
@snacktavish will soon have automatically generated gene trees.
Brian O'Meara has some very large trees for which he has/wants to have the OTU mapping…
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Hi,
I ran inferCNV and got "infercnv.observations.txt" file. In the file, there are CNV values for just 1,089 genes. It seems that the genes that have zero CNV values across cells were filtered ou…
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Hi,
I have used toytree in the past to generate cloud/densi trees from multiple gene trees. when trying to use it this time i get multiple errors (AttributeError: toytree has no attribute draw_clou…
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Hi Uyen,
Many thanks again for implementing the "whitelisting" option! I would like to ask whether it would also be possible to implement an option to partition TreeShrink analyses by clade. In my …
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Hi there!
I am having an issue with achieving the duplication and loss rates for my dataset. I have 7-10 distantly related species (>200 MYA divergence time) for each and I am analyzing 8 genes for…
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The CLOUD is an amazing tool for predicting the fate after gene duplication.
I ran it with example data and it worked well.
But when I tried to use my own data, I ran into considerable trouble:
…
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When I use orthofinder to analyze 18 species, I always can't get the contents of Gene_tree、orthologues 、Species_Tree and MultipleSequenceAlignments four files. The command I use is as follows: orthof…
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Hi Liang,
I have gene trees consisted by 106 species. When I run the `mp-est v2.1`, the segment fault occured. I applied `mp-est v2.0` using the same control file and gene tree files without erro…
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What steps will reproduce the problem?
1. 20 species (is this too many?) 3 mit genes and 2 nuc genes unliked
models all with gtr estimate freq and gamma+i none are partitioned by
codon. Only one i…