Joseph W. Brown
Joseph W. Brown
It is nice that BAli-Phy is [available using package managers](http://www.bali-phy.org/download.php). However, it is not available on the current Ubuntu LTS release (v18.04). Is it possible to make it available from...
Perhaps it was just me, but when I typed `yarn` Ubuntu suggested: ``` Command 'yarn' not found, but can be installed with: sudo apt install cmdtest ``` which, of course,...
I am exploring the heterotachy models with IQ-TREE v2.1.1 (64-bit Linux). Things run correctly for `-m GTR+H4` and `GTR+FO+H4`, but crash with `GTR+FO*H4`: ``` $ iqtree2 -s All_loci_no_ambig_no-outgroup.phy -m GTR+FO*H4...
Found investigating #143. `pxaa2cdn` won't work if nucleotide sequence lengths are not a multiple of 3 (codons). However, `pxtlate` will translate as much as it can, and just disregard any...
Other formats work, but not phylip for some raisin: ``` josephwb@Potiphar-Breen:baits$ cat foo.fa | pxlssq File type: fasta Number of sequences: 4568 Is aligned: true Sequence length: 2571 --------- Nucl...
The reverse of `pxcat` (concatenating sequences). Using some partition file (RAxML-flavour, or Nexus?) decompose an alignment into separate alignments (i.e., genes).
Almost certainly from something I did. It takes so long that travis CI would time out and fail (part of the reason we are now using GHA). I will look...
Not sure why this is happening. It was extreme enough that travis would bail and report failure. Builds locally and on GHA, tho.
Not sure why, but for a certain data set `pxcomp` is looping forever. The [stopping criterion expects a small number](https://github.com/FePhyFoFum/phyx/blob/master/src/comp_test.cpp#L271-L282), but this value becomes `-nan` and so never completes. This...
Pretty simple, but very useful! User will provide a tree file and a minimum threshold: any edge with support < threshold gets collapsed.