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How to run HYPHY on multiple files non-interactively?

TL;DR I made the following bash script to generate an input file for HYPHY. ...
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4 votes

Which sequence alignment tools support codon alignment?

I don't know of any transcript-to-transcript aligners that are able to do this, but LAST can align transcript queries to protein reference sequences using a specified frameshift cost. Here's the ...
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3 votes
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Are codons in RNA layered? Are we misinterpreting RNA codons?

This relates to the concept of the reading frame, which is the point at which you start dividing 3-letter sequences into codons. As you point out, there are multiple ways to divide a string of amino ...
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3 votes

How can I calculate the silent mutation for each position in codon?

Calculate in this context would just mean determine. You don't actually have to change every base to determine whether a change ...
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2 votes

Which sequence alignment tools support codon alignment?

Try MACSE v2 (https://academic.oup.com/mbe/article/35/10/2582/5079334) will align multiple protein-coding nucleotide sequences based on their amino acid translation while allowing for the occurrence ...
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2 votes

Which sequence alignment tools support codon alignment?

Virulign does this for virus sequences, the publication is available here and github address here
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2 votes

Pipeline for extracting gene from multiple genomes for use in HyPhy selection analyses?

Okay well, because you're using HYPHY, you're going to need a gene tree of every gene you intend to analyze. This requires you to understand the homology relationships between the genomes at hand. ...
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2 votes
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Codon usage analysis for whole genomes

This python script will remove all stop codons from your fasta file. I called it remove_stops.py ...
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2 votes
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How to convert Sars-CoV-2 ORF1ab codon positions to ORF1b positions?

ORF1ab:4588I corresponds to ORF1b:187I so one needs to subtract 4401 to go from ...
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2 votes
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Fitting branch models with godon

Branch-models are currently not implemented in godon. In the PAML manual Ziheng Yang writes: This model is very parameter-rich and its use is discouraged. This was one of the reasons I did not ...
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1 vote

list comprehension and codon translation

You need to iterate over the sequence 3 characters at a time and you need to stop when you hit the stop codon (or before for an invalid codon, e.g. of length 2). Here is a memory efficient ...
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1 vote

Are codons in RNA layered? Are we misinterpreting RNA codons?

To add complexity to this discussion, there are examples in some mitochondrial genomes where the stop point of a gene is based on the polyA-attached transcript, rather than the genomic sequence. I ...
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1 vote

panic: division of zero by zero or infinity by infinity error when running GODON positive selection analysis

Ah wait you mentioned a branch sites test, right that makes sense. You've got two or more identical sequences in the analysis. Ensure there are no identical sequences in your alignments and ... PRESTO!...
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1 vote
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What are the p01sum and p0prop parameters in godon?

Disclaimer: I'm the author of godon. The question above comes from the real communication with a software user. In the godon implementation of the branch-site model I performed the following ...
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