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A user recently sent me a tree and was astounded by what he is seeing in PATRIC, so I had to tell him that I always take the newick file and visualize the tree in FigTree due to this problem, but its …
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Dear hyphy community:
I'm a new one to use hyphy and going to use BUSTED-MH to estimate positive selection anaysis.
However, it runs too slowly, is there any ideas to push the running? BTW, my …
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Our MOO implementation (NSGA2) is slow!
It tries to minimise MSE and number of nodes in the tree.
I'm not sure, but maybe it's creating a derivation tree for every individual... this shouldn't b…
jmmcd updated
2 years ago
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In [rna-seq.tex](https://github.com/klmr/thesis/blob/master/rna-seq.tex) you have excellent discussion of various aspects of expression quantification. I think there are some missing pieces:
- Given t…
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Hello,
I am using PRICE software, it is really a wonderful tool, I have used it to predict ORF of several samples and it works well. Unfortunately, now I encounters a problem when analyzed a sample. …
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Hello,
I have a refseq gff that contains two chromosomes in it which I wanted to use in the panaroo pipeline. I tried using the script to convert it to a prokka gff but I get only the second chromo…
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Hello,
I am using SNPGenie for a Genome-wide SNPs dataset of 70 individuals of a haploid organism consisting of 14 chromosomes, using as input a VCFfile. For the requirements of the tool, I have sp…
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Installed codon (0.16.3) with `/bin/bash -c "$(curl -fsSL https://exaloop.io/install.sh)"`
Created a `fib.py` with
```
def fib(n):
a, b = 0, 1
while a < n:
pri…
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The `expandaln` command fails to properly read index, producing an '`Invalid database read for database data`' error
## Expected Behavior
Command to run without error messages.
## Current Beh…
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HI there,
I am using MoAIMS for my m6a data analysis. I got the following error while using my samples as well as test data provided by the authors:
#Fit models.
Error in crossprod(rV %*% t(db.dr…