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Hello,
First I wanted to thank you for the work you have done with this package. This is my issue (connected with #302 but I did not see a solution there):
**Describe the bug**
I am trying to …
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Dear author,
I am very interested in the methodology proposed in your work. Could you please provide some insights into the functions of neigh_cons_score.py, genomic_context_conservation_table.py, …
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I ran PIRATE with 322 genomes (gff files) as input, but the file indicates 321 genomes. Is there any way to investigate why the count decreased from 322 to 321? The confirmation details are as follow…
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I have questions about options in https://github.com/SionBayliss/PIRATE/blob/master/README.md
## Usage
### Basic examples
- `-a|--align`
- `-r|--rplots`
Running PIRATE with the options `-…
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This is a request for a new feature rule to use PPanGGOLiN to create pagenome graphs for the genome projects.
I think we should use the Roary-defined Gene Famillies as input to `ppanggolin`. This w…
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Trying to get the script to complete, I and tried bigscape version 1.1.8 (from a conda install) as well as from a docker images hosted by biocontainers [here](https://biocontainers.pro/tools/bigscape)…
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Do the necessary plumbing so that MMseqs2 can be used for clustering. Evaluate those clusters on glycine7 and glycine33 in peptide space first. Compare histograms out cluster sizes to BLAST and usea…
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Hi David,
I was recently using OrthoFinder to look for species-specific orthogroups in a new genome that we've assembled. However, I noticed that several of the orthogroups classified as species-sp…
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After run_mcl and get_clusters, I found that one node belongs to two clusters. Is this method doing a soft clustering?
hw449 updated
7 months ago
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Hi David,
I devoted in gene families in maize.To identity the paralog of Sn2k gene family in maize,I ran orthofinder with 20 different species.I got maize-SnRk2 protein by using Arabidopsis thaliana…