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Hi all,
we finally installed 2.4.0-alpha.2 and it seems to work differently than before. Also I do not really everything in the hel message:
1) I wanna run busted (with a lot files)
a) first in b…
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Following [this tutorial](https://github.com/soedinglab/MMseqs2/wiki#how-to-create-a-target-profile-database-from-pfam) to use PFAM database with mmseqs.
So, I follow the steps below:
```
curl ht…
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Dear all,
we want to do something like described in Ebel et al. 2017
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007023#sec013 (see Estimating adaptation). Since BS-.RE…
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**[Original report](https://bitbucket.org/pycogent3/cogent3-dev/issue/24) by GavinH (Bitbucket: [557058:e40c23e1-e273-4527-a2f8-5de5876e870d](https://bitbucket.org/557058:e40c23e1-e273-4527-a2f8-5de58…
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## Expected Behavior
Precompute mmseqs index tables are generate using `createindex`
## Current Behavior
Fails after a few minutes of computation with the following error message:
**indexdb died…
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## Expected Behavior
It was working before. Same database and protein sequences
## Current Behavior
:(
## Steps to Reproduce (for bugs)
Please make sure to execute the reproduction steps with…
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Hey,
I am trying to detect recombination in some codon alignment. However, after a few hours, datamonkey send me an email in which says the following:
Your analysis for 5b9a4a2da913185b60116395…
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I can find the following buried in the pepr.log report:
2018-08-16 17:41:17 INFO PhylogenomicPipeline2 - taxa: 46
2018-08-16 17:41:17 INFO PhylogenomicPipeline2 - genes: 132
2018-08-16 17:41:17…
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See: [JBrowse link](http://www.fireflybase.org/jbrowse//?data=Ppyr-data&loc=Ppyr1.3_LG3b%3A20692601..20707800&addFeatures=%5B%7B%22seq_id%22%3A%22Ppyr1.3_LG3b%22%2C%22start%22%3A20694168%2C%22end%22%3…
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From Morgan Jackson
I'm trying to run a partitioned analysis of DNA and CODON data. My partition file is as such:
```
#nexus
begin sets;
charset rDNA1 = dna.phy: 1-1022;
charset rDNA2 = d…