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Hi,
It's not clear to me how SNPgenie polarizes the mutations (to compute dN/dS and piN/piS).
Does it assume the ancestral states are the ones supplied in the reference fasta? If so, how would S…
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Hi,
This should be a simple fix. When I try running the following in R:
system('vsearch --usearch_global 16s_13_5_precalculated.tab --db 97_otus.fasta --matched 16s_13_5_precalculated.tab --id 0.…
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We should run a Bayes Factor test for strict vs uncorrelated lognormal clocks. I don't think that we have enough data to support a more complex model, but worth checking out.
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### Context
`augur clades` currently places clades by finding the biggest branches on a tree that satisfy each clades defining mutations as provided by the user.
This method has a few downsides:…
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Hi there,
I've been using Historian to reconstruct the ancestral sequences within multiple different sequence data sets. My largest data set, which contains roughly 1000 sequences, has been unable…
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Dear PRANK developers,
As the title indicates I am experiencing that there is a mismatch of the labels between the tree and fasta file containing the ancestral sequences. The following picture show…
krdav updated
6 years ago
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Thanks for developing this use of PICRUSt! Your idea of dynamically retraining based on dada2 reads is a great fit for any program that does not use 'close-ref' OTUs. I think this method could be wild…
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Hi Nick,
I'm using Gubbins v3.3.5 as indicated below:
```
run_gubbins.py $PREFIX-CLEAN_NoRef.aln --first-tree-builder iqtree \
--tree-builder iqtree \
--tree-args " -T…
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Hi Andrew,
I would like to add Ancestral allele info to my vcf file, so I would be able to get the derived allele for my site frequency spectrum. I was running a command:
python /homeappl/home/cui…
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Some ideas from a chat with Fred Jaya. Use the wiki to give a few examples of simple benchmarks, e.g.
1. RaxML vs. IQ-TREE on individual loci (fix models to be equal, assess trees in one piece of s…