Romain Derelle

@Logan1x I have abandoned Mauve, which doesn't seem to work well. It is actually easy to get a list of SNPs from Minimap2 (using third party pgm provided in the...

Thanks. You are right (install was flawless on my linux desktop). I have managed to install parasail on my Mac by adding the following code to the setup.py file: import...

There might be a quick fix: `tmp_allelic_dp = [x[1]/(x[0]+x[1]) for x in barcode_support[l] if x[1]>5] ` and then add a threshold for a minimum number of barcodes.

Thanks for pointing this issue. I've only used Python 3.6 and wasn't aware of this bug. I will change the readme file to point to Python 3.6 / 3.7 (instead...

Hi Matt, the problem comes from FastTree, which is unable for some reasons to analyse the file alis_27.phy. Since you have already run Broccoli, I assume you are using the...

My apologies for this late reply. "nb_reduced_prot" refers to the number of proteins that are filtered after the first k-mer clustering step and that are then used in the following...

Hi Matthew, thanks for sharing your data. I have fixed step 2: now, Broccoli will not stop even if one pair of species does not yield any phylogenetic analysis. Please...

Hi, could you please run the diamond command line and post here the output (error message): `diamond blastp --quiet --threads 1 --db dir_step2/databases/61.db --max-target-seqs 6 --query dir_step1/24.fas --compress 1 --more-sensitive...

Hi Jesse, my apologies for this late reply. It might be due to the new version of Diamond you are using. What the files in dir_step2 and dir_step3 look like?...

Hi, the ML option is **extremely** slow. NJ trees take about 0.2s while ML trees take about 10s to be computed, and Broccoli performs hundreds of thousands of phylogenetic analyses....