Sergei Pond

Dear @Emilyaoc, `contrast-fel` is a standard analysis. You can run it like so ``` hyphy contrast-fel --alignment my_alignment.fas --tree my_tree.nwk --branch-set my_label ``` The actual batch file is in (if...

Dear @Xiaojun928, What C/C++ compilers are you using? Best, Sergei

Dear @Emilyaoc, For analyses that support multiple partitions you specify it like so ``` --branch-set label1 --branch-set label2 ... ``` Best, Sergei

Dear @Emilyaoc, Two sets of branches. `contrast-fel` will not consider "nuisance" branches for testing, so whatever you leave unlabeled should not contribute to the analysis. Best, Sergei

Dear @Xiaojun928, Looks like this is a GCC bug ([missing intrinsics](https://gcc.gnu.org/bugzilla/show_bug.cgi?id=80582)) for versions prior to version 8 (the current version is 12+). Is it possible for you to upgrade to...

Dear @Xiaojun928, Try version 2.5.46 (just released). I replaced `_mm256_loadu2_m128d` with a different instruction that is supported by older (pre 10) GCC versions. Best, Sergei

Dear @Xiaojun928, My apologies. I managed not to commit the compilation fix to `2.5.46`. It is in the `develop` branch now. Please give it a try ``` git clone https://github.com/veg/hyphy.git...

Dear @Xiaojun928, Making progress. This is a different error. Let me look into that; just to check -- what is the GCC version for the latest error? Best, Sergei PS...

Dear @yashsondhi, With stock analyses with no changes at all you can do something like this. Let me know if this helps/makes sense. You can estimate **per-branch** `dN/dS` using [FitMG94](https://github.com/veg/hyphy-analyses/tree/master/FitMG94)....

Dear @1221li, In your actual example, the p-value for the test is **not** significant (p~0.4), hence `K` is **not** significantly different from 1. RELAX will fit several models and each...