SHOOT
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davidemms
SHOOT.bio - the phylogenetic search engine
Hi David! I'm trying to run python create_shoot_db.py command to my local data. The code looks like this: python create_shoot_db.py /mnt/c/Users/uzunm/mydata/OrthoFinder/Results_Mar30_5/ I got the comment "Args: input_directory [full,profiles]." What does...
when I run: python shoot candidate_sequences.fasta OrthoFinder/Results_Mar28/diamond_all_sequences.subtrees.fa I get the following error Traceback (most recent call last): File "/home/........./envs/orthofinder/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/home//........./anaconda3/envs/orthofinder/lib/python3.9/runpy.py", line...
This version supports multiple query genes and provides outputs by matching OGs. There are small changes in the output files: - added a ".sh.map" file for correspondance between original query...
Hello, I was wondering if this is possible to use shoot with existing database of multiple alignment and trees. Let's say that I reproduce the same directories as orthofinder and...
By default, SHOOT outputs a serie of files in the same directory as the input FASTA file. This PR changes that behavior so output files are by default put into...
Hi, I was wondering if the SHOOT website has an API or some way to submit proteins via command line? I have a few hundreds genes I'd like to run...
The "Material and Methods" section of the SHOOT publication (https://doi.org/10.1186/s13059-022-02652-8) , mentions "..the OrthoFinder version 3.0 option, “-c1,” was used to cluster genes into groups consisting of all homologs, rather...
Dear David, Is there an open access to the database used for the online version? Thanks a lot ! Benoit Durieu
Hi! I'm trying to run the following code in a shoot database I've created: python shoot lefty1.fasta /storage/.../orthofinder/Results_Oct03 Traceback (most recent call last): File "/storage/.../miniconda3/envs/bioenv/lib/python3.9/runpy.py", line 197, in _run_module_as_main return...
