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Hi,
I'm trying to run on the example dataset using the command
`python ~/Broccoli/broccoli.py -dir ~/Broccoli/example_dataset/ -ext '.fasta'`
with diamond version 4.0.515 and fasttree versio…
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Hi @sdwfrost I saw the paper you linked to (https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14038), I'm just putting this here as an interesting project for myself later. It seems li…
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**Stephen Owen** 6 months ago
Is this possible? Surely
Some differences are very simple, just having a few species change genera, but even this can be impossible, for example, if the alternate phy…
i2xzy updated
5 years ago
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Hi,
I have multiple samples from an experiment that have ~6000 cells of 10X scRNA data each. If I were to try and run NUMBAT on the entire merged experiment the BAMs would be too big.
Is it po…
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Hey, I love the data you're compiling. What project are you working on? I don't want to accidentally steal any of your ideas or discoveries. But if it's possible, I'd like to test a new phylogeneti…
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Hello,
We recently used TreeTime to infer ancestral sequences for a set of Influenza samples and then visualized the phylogenetic tree with the branches being annotated by the inferred mutations.
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In b7cfc9b03059ef2200e738a079fedfbc8f5e7e19 I fixed a bug in Grid.speciation which occured when the fission parameter was set to 1 (every second individual becomes part of the new species) or 2 (geogr…
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see the text file Avonet_traits.txt
There are columns Sequence Avibase.ID1 - do these help you get the phylogeny
I had to change some of the bird names to match the original data - see the av…