Run poseidon with mitochondrial sequences

rnajena / poseidon

PoSeiDon: positive selection detection and recombination analysis pipeline

MIT License

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Run poseidon with mitochondrial sequences #27

Open pedronachtigall opened 3 years ago

pedronachtigall commented 3 years ago

Hi @hoelzer,

First, thank you for designing this nice tool. I want to use poseidon in a set of mitochondrial genes, but, apparently, poseidon only uses the Standard Code. Is there an option to decide the translation table used (e.g., set the Vertebrate Mitochondrial Code)?

Best regards, Pedro

hoelzer commented 3 years ago

Hi @pedronachtigall

thx for your interest in the pipeline. Yes, at the moment PoSeiDon only uses the standard code. I think there are different steps where I would need to adjust that (codon-aware alignment via TranslatorX, CODEML, ...) but should be possible. I will set it on my todo but unfortunately, this will need some time.

pedronachtigall commented 3 years ago

Hi @hoelzer

Please, let me know once you have implemented this into poseidon.

Best, Pedro