Sergei Pond

Dear @ddf37, Thanks for providing the error-triggering tree. Sequence names that start with a number should be OK. What HyPhy will **not** accept are strings like `NC_005042.1_1267363-1268583`, because `-` would...

Dear @dongzhang0725, Do you have different coding tables in the same alignment, or do you have several alignments with different coding tables? In the first case, you have a situation...

Dear @dongzhang0725, I would suggest you split the datasets by genetic code and do a joint analysis on them; combining them in a single tree (if the clades are fully...

Dear @dongzhang0725, Great, this makes sense. Would you be able to send me the picture of a tree showing your Test/Reference branch sets and also which of the taxa use...

Dear @dongzhang0725, Quite an interesting problem. Since you have a very deep deep (11,000!), I would suggest you do subtree analysis. Here's why. 1. Computational performance: both `aBSREL` and `RELAX`...

Dear @dongzhang0725, If you are interested in comparing selective pressures between groups of branches at the level of the entire alignment, consider [BUSTED-PH](https://github.com/veg/hyphy-analyses/tree/master/BUSTED-PH). If you are interested in comparing selective...

Dear @dongzhang0725, Unfortunately, these internal errors are impossible to diagnose without running the data and recreating the fault condition. Would you mind sharing the file with me (privately by e-mail...

Dear @dongzhang0725, There is indeed an issue with this dataset (some calculations were making larger than expected numerical errors), but you should be able to run it to completion (I...

Dear @andreaniml, There are many ways to do it (you can write a Python script etc). My preferred method is to use [jq](https://stedolan.github.io/jq/), with which you can do the following...

Dear @LesterJP, I can't see to find this particular ticket number. Would you happen to have the URL of your job page? It will look something like https://www.datamonkey.org/absrel/65978ad3ba6f2072cc42906e (different long...