5
votes
Accepted
How to run HYPHY on multiple files non-interactively?
TL;DR
I made the following bash script to generate an input file for HYPHY.
...
- 2,735
3
votes
Accepted
How can I use Arlequin via the command line?
For MAC OSX, the executable found in arlsumstat_macosx (arlsumstatmac_64bit) seem to work appropriately. The directory for ...
- 203
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. ...
- 347
1
vote
Accepted
Measure the purifying selection for certain taxa along a phylogeny
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 ...
M__♦
- 13k
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!...
M__♦
- 13k
1
vote
Accepted
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 ...
- 2,735
1
vote
PAML branch-site model: Identical lnL value between null and alternative models?
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 ...
M__♦
- 13k
1
vote
How can I use Arlequin via the command line?
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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