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I asked in Slack if there was a way to use anvi-get-enriched-functions-per-pan-group to do functional enrichment on bins in a collection instead of on groups of genomes in a pangenome. Meren thought i…
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I am running poppunk on a large set of sequences that essentially lack any accessory gene content. I can complete the first step fo generating the DB, but when trying to run an initial model fit, I g…
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Hi,
I am using POPUNK to study 27 genomes of a bacteria downloaded from NCBI. But whenever I run this command,
`root@hon-pc:/home/fuan/monas/fna_combine# poppunk --easy-run --r-files reference_li…
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Say a have a gapped alignment
```
ATGTAGTC
ATG--GTC
ATG-TG-C
```
Is it possible to use Treetime to construct a dated phylogeny? I would like to not drop columns with a gap.
The use case i…
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Hey, I tried to apply Poppunk on MAGs. As no one has mentioned it before I wanted to ask if there is a problem with that. I know that sketching is regularly used with MAGs.
On my data, I get almos…
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Hi, Meren. Thanks for your programe. Following the tutorial of pangenomics, I got a summary *.txt. However, I found that some gene clusters usually correspongded to same COG id, such as the following …
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Hi,
First, thanks a lot for providing and maintaining macsyfinder, it's a very useful resource!
I stumbled upon what I think is a bug. I was running macsyfinder with `unordered` and `ordered_replico…
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Dear developer,
I tried to identify core loci of plasmids belonging to IncP-1 groups (ACCESSION: `BN000925 U67194 AB231906 AM157767 GQ983559 AM261282 AY950444 KC170283 KP324830 KX377410`)
Runn…
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Hi all
I am trying to run poppunk v2.0.2 using "poppunk --easy-run --r-files reference_list.txt --output poppunk_NON --threads 20 --plot-fit 7 --min-k 15 --max-k 31 --k-step 2 --full-db --ignore-leng…
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Hi
I'm trying to setup get_homologues-est with my cluster. I have followed the instructions from here: https://hub.docker.com/r/csicunam/get_homologues using Docker to setup. I've mounted my local …