jsoghigian

Is there a way to modify the stringency/match settings for adapter detection and trimming? I have an adapter fasta from long read (HiFi) data and those adapters are present in...

Feature Request: Import MCMCTree Result Tree (PAML)

4

Thank you for the excellent packages! I was wondering if it would be possible to implement functionality that would enable the importing of MCMCTree 'nexus' result trees, and their subsequent...

Diagnosing pipeline failure

11

Hi there! Thanks again for the great tool. I've been trying it on my personal data and I think it is finishing the OrthoFinder step now. I am not sure...

removeElem error

1

Hi, Trying to use this tool on a sorted BAM file to subsample to a much lower coverage for testing. I'm getting the following error from the below command: variant...

prefix flag causes crash

1

Hi there, I think the prefix flag is causing a crash... When I run this command: > $ rd --msa $msa --tree $tree --threads 20 --prefix $prefix I get this...

create_files_for_hogs.py error

1

Hi, We were trying to create HOG files with create_files_for_hogs.py and ran into the error "csv_read_mode" not defined, as below: ``` Traceback (most recent call last): ... File "/path/to/create_files_for_hogs.py", line...