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Hi.
**I am trying to perform a Ks analysis comparing a species of interest with two others. I was able to generate the configuration file below.**
```
[SPECIES]
focal_species = poatr
# info…
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Submitting Author: Semidán Robaina (@Robaina)
All current maintainers: @Robaina
Package Name: Pynteny
One-Line Description of Package: Query sequence database by HMMs arranged in predefined synteny…
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An error submitted to me by email using `hybpiper gene_recovery_heatmap` that the plot area was too wide. The script calculated it needed 87550x2300 pixels but apparently matplotlib has a limit of 655…
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Dear Jacob
I used orthofinder for gene family clustering of five species (Ab, Ad, Ak, As, Lo). Then I would like to use orthoSNAP with default parameter to classify multi-copy gene families. But ther…
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Hi, @lh3
I use `pangene` to run with Arabidopsis pangenome for idenitifing complex gene clusters. But I couldn't really understand why the overall graph is a hairball (also in the HPRC graph Zenod…
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Hi!
Great software. I wish to know the meaning of the header in the `codon.fasta` output:
For example:
```
>ENSGALT00010053003.17 | CODON | REFERENCE
>ENSGALT00010053003.17 | CODON | QUERY
`…
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Hi!
I'm running TOGA for human and betta fish genome but it failed at STEP 7: Execute CESAR jobs. It can only excute one nextflow job and then kept reporting like this `NOTE: Process 'execute_jobs …
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I am using Panaroo on 100 _E. coli_ isolates using different parameters and I am validating the gene presence/absence matrix using a subset of genes (genes starting with **_tra_**). It seems that ofte…
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Dear Fukushima-sensei,
Thank you so much for writing the CSUBST program and providing such detailed documentation as a part of the paper. I have been trying to run CSUBST on my own data and have en…
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This is the error I am getting which makes no sense to me.
File "/gpfs01/home/user/miniconda3/envs/panaroo/bin/panaroo", line 10, in
sys.exit(main())
File "/gpfs01/home/user/miniconda3/…