hyphy-analyses
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veg
HyPhy standalone analyses
Dear @spond, When using BUSTED-PH to test for episodic diversifying positive selection in certain foreground vs background branches, we were surprised to see that the results in foreground and background...
Hello! Im trying to remove duplicate sequences using https://github.com/veg/hyphy-analyses/tree/master/remove-duplicates. It all works well when I run it on the example files, or only on one of my alignments. However, I...
Dear hyphy users and developers, I found it really convenient for using this tool to identity selections among species. Here, I face an issue and hope you to help me...
[N9.HOG0000289_tree.labeled.txt](https://github.com/veg/hyphy-analyses/files/13653348/N9.HOG0000289_tree.labeled.txt) [N9.HOG0000289.pruned_tree.txt](https://github.com/veg/hyphy-analyses/files/13653349/N9.HOG0000289.pruned_tree.txt) [test_list.txt](https://github.com/veg/hyphy-analyses/files/13653353/test_list.txt) Input and output files are attached. The function call is below. Maybe I could use the `--reroot` flag and give it the original root, but I just...
Hi, Is there a way to estimate gene-wide dN/dS on a set of test foreground vs. background branches for several genes as done in these two papers. I have attached...
Hello, Thanks for such a great tool for phylogenomic analyses! I was wondering if there was a way of labelling the branch of the last common ancestor of two species...
Dear Dr. Pond, This is Xiaojuan Li，I have calculate dn and ds using FitMG94, which reported trees scaled on expected number of synonymous and non synonymous substitutions per codon. But...
Hello, I am trying to run RELAX-scan using HyPhy 2.5.51 but it immediately crashes. I then tried HyPhy 2.5.32 and managed to get it running. I am attaching the log...
Hello there, I have previously used BUSTED-PH successfully on ~500 seqs. Now, I was trying to improve the analysis for a publication and I managed to get up to ~1500...
Dear hyphy community: I'm a new one to use hyphy and going to use BUSTED-MH to estimate positive selection anaysis. However, it runs too slowly, is there any ideas to...
