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Moving https://github.com/iqbal-lab/mykrobe_paper/issues/60
> "There's a function called create_mask which does a malloc and returns that object, but I don't think that object is ever freed."
Yes, t…
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Hi,
I am running pyrad on a grand total of 6 samples, and it has been running for almost 2 weeks with little to show for. Specifically I am running it on a HPC cluster with this bash shell:
# !/bin/…
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this just occurred to me while I'm running a workshop on Bayesian phylogenetics.
We can make a parameter plot for trees, that will be comparable with the traces you get for continuous parameters. To …
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Hi, after `Pkg.update()` and `using Atom` gives
```
julia> using Atom
INFO: Precompiling module Atom...
ERROR: LoadError: LoadError: ArgumentError: AbstractTrees not found in path
in compilecache at…
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This is important, since the version we are currently using contains a **BUG** that allows for negative branch lengths in trees constructed with the Neighbor Joining algorithm and another bug that inc…
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Methylation would be nice if it were added. More tools are coming up in that area now.
`Error: Invalid value for "--category": invalid choice: Methylation. (choose from Assembly, ChIP-seq, Combinator…
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I have come across several examples where specimens are linked as vouchers to publications, but these publications do not show up in the related projects that collected or used the specimen. Shouldn't…
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For deeply silly reasons, it has become conventional in phylogenetics to represent spaces as underscores in taxa names (e.g., _Homo sapiens_ would be `Homo_sapiens`). Owing to this historical blunder,…
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Following on from a discussion with Tanya and Antonia....
The APC is inhibited by various CDC20/fizzy family inhibitors at various cell cycle phases (not clear cut, sometimes overlapping).
Our first…
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## Phylo code review - 20th April 2014
### General notes
Overall very good, and a great start for the Bio.jl phylo module. Here I have attempted to map out what would be required to get to a version …