hyphy-analyses
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veg
HyPhy standalone analyses
Dear hyphy team, I would like to use SCUEL-WG tool on HIV whole genomes we have generated so that we can study their subtype and the presence of potential recombinants....
Hi @spond @stevenweaver et al In the old batch files, there used to be an option to turn off rerooting of trees: ``` _DO_TREE_REBALANCE_ = 0; ``` I've tried adding...
Hi HyPhy team, I have been using HyPhy analysis( RELAX, BUSTEC, BUSTED ) in my research to study molecular evolution for the past two years. I have some issues in...
Hi, I'm using MEME and FUBAR in a dataset of 6 species, but I'm most interested only in one. I'm wondering if for that species I should include all the...
Good afternoon, I want to check that I'm understanding the results of BUSTED-PH correctly. If I obtain the following set of p-values: - test results p-value: >0.05 - test results...
Hello, I have a question regarding the output for the FitMG94 model with separate dN/dS calculations for each branch (--type local). Would it be possible to output the raw counts...
Hi, I am trying to understand the output of the FitMG94 model with per branch calculation (--type local). For example, the output for one node is: "Node20":{ "Confidence Intervals":{ "LB":0.05288894421311353,...
Hi, I can't figure out how to install and run RELAX-scan. I have downloaded and installed hyphy-analyses as explained in this ReadMe: https://github.com/veg/hyphy-analyses. All 21 tests executed by "make test"...
Hi, Hyphy team. I'd like to set one or two specific foreground branch to test using BUSTED-MH. My code is: **hyphy BUSTED-MH.bf --alignment filter.fasta --tree tree.tre --srv Yes --branches A**,...
Hi, I am investigating selection efficiency on set protein coding sequences and have applied RELAX to see the relative intensity on test branches compared to reference with some unclassified branches....