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TL;DR I made the following bash script to generate an input file for HYPHY. #!/bin/bash cat << EOF inputRedirect = {}; inputRedirect["01"]="Universal"; // genetic code inputRedirect["02"]="$(readlink -f $1)"; // codon data inputRedirect["03"]="$(readlink -f $2)"; // tree inputRedirect["04"]="${3:-All}"; // Test for selection on a branch inputRedirect[...


3

For MAC OSX, the executable found in arlsumstat_macosx (arlsumstatmac_64bit) seem to work appropriately. The directory for arlsumstat_macosx does not contain any examples but you can use example files from arlecore_macosx/Example files_linux using this syntax. The complication is that arlsumstatmac_64bit will look in the current directory for the file ...


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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. Depending on your project, you might already have a list of homologs you're trying to analyze, or you can start from scratch. If starting from scratch, you will ...


1

The following is not the clearest explanation of dN/dS humankind has seen, but I hope you get the gist and core idea of likelihood is absolutely correct. I am wondering if you are thinking of a different test to the way I would do this calculation. This ain't a text book clarity answer. Anyway what you are proposing is a likelihood ratio test (LRT) for ...


1

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! It will work :-) Below are my original thoughts before I re-read your question. I've kept the notes because it helps explain the theory a bit. There is no ...


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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 reparametrization: $p_{01sum} = p_0 + p_1$ $p_{0prop} = \frac{p_0}{p_0 + p_1}$. This has the following advantages: Both parameters have a well defined range $(0, 1)$...


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The issue with PAML is that it doesn't throw many exceptions (programming jargon for trapping and reporting errors) if something is wrong, generally the "exceptions" are identified in the failure to report an expected value in the output. Possible explanation fix_omega is not turning the omega parameter on or off it is simply defining what the value of ...


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A concise description for using Arlecore on terminal for MAC, LINUX or Windows is provided here: http://cmpg.unibe.ch/software/arlequin35/man/arlecore_readme.txt


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