FEL ANALYSIS doubts

[Naniogui]

Congratulations! The datamonkey family increased.

I need help to understand the job 66f6dd49de2c0658dec4fe5d because:

1. The submitted file had 91 cds but ntax=80;
2. The alignment has 280 "codons" but nchar = 804 (~268 codons). I expected that the number of sequences and the number of codons were the same in the analysis. So it is hard to me understand what site is neutral, diversifying or purifying regarding to the amino acid sequence in the proteins. If you explain me what taxes have been deleted and what codon counting to the analysis, it will be easier for me. Sorry but IT is hard for me. Thank you very much for the patience.

[spond]

Dear @Naniogui,

Could you please attach the alignment you are submitting as a txt file? Datamonkey does not retain raw files, only what has been filtered, so it's impossible for me to explain what took place.

Best, Sergei

[Naniogui]

How fast!

Thanks.

Nancy Oguiura @.*** Pesquisador Científico Lab. Especial de Ecologia e Evolução Instituto Butantan Av. Dr. Vital Brasil, 1500 - CEP 05503-900 São Paulo - SP - Brazil tel. (55)(11) 2627-4698

Em sex., 27 de set. de 2024 às 14:53, Sergei Pond @.***> escreveu:

Dear @Naniogui https://github.com/Naniogui,

Could you please attach the alignment you are submitting as a txt file? Datamonkey does not retain raw files, only what has been filtered, so it's impossible for me to explain what took place.

Best, Sergei

— Reply to this email directly, view it on GitHub https://github.com/veg/hyphy/issues/1747#issuecomment-2379785102, or unsubscribe https://github.com/notifications/unsubscribe-auth/BLVF4O3BMMS4ABGAH4WYPJTZYWLSTAVCNFSM6AAAAABO7TZNUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZZG44DKMJQGI . You are receiving this because you were mentioned.Message ID: @.***>

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[spond]

Dear @Naniogui,

I should have mentioned that if you send an e-mail attachment, GitHub will not forward it. Could you please use the web form at https://github.com/veg/hyphy/issues/1747 to attach a file to the message?

Alternatively e-mail it to me at spond at temple dot edu

Best, Sergei

[Naniogui]

91cdsSerinosBioeditFasta.txt

[spond]

Dear @Naniogui,

This fasta file uses a non-standard character for gaps (~). BioEdit used to do that. HyPhy strips them out completely. The solution is to replace all ~ with -. After than, the number of codons in the resulting file is 311. In addition, Datamonkey will remove all duplicate sequences (of which there are 11 in your alignment). The results are at https://www.datamonkey.org/fel/66f6f63ede2c0658dec4ff35

Best, Sergei

[Naniogui]

Thank you very much :)

These details drive me crazy!

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