Chris Wymant

I get an error with `iqtree-1.6.12-Linux` when specifying a particular kind of output file prefix: ``` $ iqtree -s AlignmentInWindow_1_to_3000.fasta # works $ iqtree -s AlignmentInWindow_1_to_3000.fasta -pre foobar # works...

Ambiguous nucleotides are treated literally by sequence_trim. e.g. specifying AAAN to be trimmed will trim "AAAN" from sequence ends, but not "AAAA", "AAAC" etc. which is probably fair enough, but...

Make the consensus files an option

1

(and update the manual)

pysam's "is_duplicate" attribute

Try to wrap together the --x-raxml args with quotation marks.

`#` instead of `\\` for comment is fatal in RStan 2.26

1

#### Summary: Using `#` instead of `\\` to begin a comment in RStan 2.26 resulted in fatal mysterious `parser failed badly` error. #### Description: I encountered this error in RStan...

RAxML failing without error message

5

Hi, I have a issue. I have up to date version. I just try to follow the example. I installed VirtualBox on my computer and ran Ubuntu 16.04.3. But on...

make save_output_files create files with all comment lines at the start

2

A simple preprocessing with `grep -v '^#'` is one way to solve this issue, and maybe it wouldn't be a simple fix inside cmdstanr if it's related to how these...