treePL
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blackrim
Phylogenetic penalized likelihood
Hi! I used treePL to analyze my dataset. I ran PRIME to find the optimal parameters and used cross-validation (CV) to determine the best smooth value. However, I ran 10...
Hi Stephen, We used several fossils to calibrate the tree, as shown below. However, the divergence times were generally much older than expected. In particular, the root time was exactly...
I encountered a problem building from source and using a non-standard path. (Specifically, this was building on an HPC system without root/sudo.) The build would fail because the makefile was...
Hi Stephen, We have a problem here, which has been seen in other posts, but we still don't know how to solve it for our own situation. Here are my...
Hi~ I have installed 'treepl' with conda (conda install -c genomedk treepl), but when i type 'treepl' it shows 'treepl: command not found', so i wonder how to call 'treepl'??...
I'm receiving a lot of "linear search failed" lines in my run of a tree with 1457 tips. What does this mean?
Hey Guys, Does treePL generate substitution rates that can be viewed somewhere? I see what looks like these rates as edge lengths in .r8s files, but I am just not...
Hi everyone, I am new to Github! I have a question related to a post that was already closed (https://github.com/blackrim/treePL/issues/31) but since I am not sure if it can be...
We have been attempting to do cross-validation with values determined from the 'prime' analysis; however, the analysis gets stuck (crashing my computer), appearing to be going in circles, printing this...
Hi, I'm having some problem installing treePL. I did install the dependecies: ``` [tk19812@bp1-login01 deps]$ ls -l total 35640 drwxr-xr-x. 10 tk19812 bisc 4096 Aug 19 09:57 adol-c drwxr-xr-x. 7...
