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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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alignment in final tree #381

Closed tbazilegith closed 11 months ago

tbazilegith commented 11 months ago

Hi Nick, I am a little bit uncertain about which alignment (masked alignment or the original one) to use in the command below. The manual doesn't specify... Any ideas? generate_files_for_clade_analysis.py --list isolates_list.txt --aln in.aln --gff .recombination_predictions.gff --tree .final_tree.tre

Thanks, TJ

nickjcroucher commented 11 months ago

See #380.