Sergei Pond

Dear @ritafonso, MEME and FUBAR are designed to work with fixed differences (not within-population polymorphism). That said, people commonly analyze some types of data (e.g. viruses or bacteria) where each...

Dear @francicco, Some of these analyses (including `RELAX-scan`) are quite noisy (complex models). The original README was test-run on a HyPhy release that is quite old and the new version...

Dear @KittyMurphy, Just that one branch? For example the orange branch in the following example? Best, Sergei

Dear @KittyMurphy, I can modify the tree labeling script to do this. How do you anticipate specifying the two species? Would something like the following work? ``` hyphy label-mrca.bf --tree...

Dear @KittyMurphy, Are you looking to label all MRCAs with the same label or with different labels? I can definitely implement something like what you suggested above, optionally with a...

Dear @KittyMurphy, Please see https://github.com/veg/hyphy-analyses/blob/master/LabelTrees/README-mrca.md Best, Sergei

Dear @KittyMurphy, Great. Please let me know if you discover any issues. Best, Sergei

Dear @sushidaren, Look inside the JSON file produced by `FitMG94.bf`. Best, Sergei

Dear @sdwfrost, You should be able to add the following line near the top of `FitMG94.bf` ``` utility.SetEnvVariable ("ACCEPT_ROOTED_TREES", TRUE); ``` Whether or not trees are automatically unrooted is still...

Dear @sdwfrost, This is not the behavior I am getting -- with `utility.SetEnvVariable ("ACCEPT_ROOTED_TREES", TRUE);` added to `FitMG94.bf` (it should not be necessary to also add it to `AncestralSequences.bf`), the...