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Is it possible to use PhyloCSF on mitochondrial genomes, i.e. with an alternative genetic code?
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Hi Mike,
I'm a PhD student in Laura Hug's lab currently working on a side project related to constructing universal ToLs. I was following your ToL example using the universal marker gene set and no…
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I'm using getorganelle to extract mitochondrial genomes from insects. I first do an assembly using SPAdes (because we use that output for other downstream tasks anyway), and then I run get_organelle_f…
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Dear author,
Thanks and cheers for developing this package!
I have the question as to how to use the package to download complete mitochondrial genomes from the NCBI. This is because I am going …
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I wonder if you are interested in developing sketches for mitochondrial or plastic genomes?
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**CHM13V2 T2T Assembly**
```bash
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.fna.gz
snipe sketch --ref GCF_00…
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1. Is REGENIE capable of analyzing mitochondrial genomes?
2. If yes, what are the parameters that I need to set to analyze mitochondrial genomes?
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I'm interested in using `mity` to assess within-individual variation in mitochondrial DNA. I have assembled mitochondrial genomes for ~300 individuals of a non-model fish species using `MitoZ` and fou…
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Hello,
Thank you for creating this great tool. I have successfully run read2tree using marker genes downloaded from OMA browser and my own data, which seems really great.
However, I found some pro…
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Hello,
I would like to assemble the plant mitochondrial genomes using Novoplasty. I read your recently published article, mentioned that RuBP used as a seed sequence for cp genome. But I would like t…