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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 to use in final tree #380

Closed tbazilegith closed 11 months ago

tbazilegith commented 11 months ago

Hi Nick, I am a little uncertain about which alignment( masked aln or the original one) to use in the command below 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

It uses the original input alignment, the script will mask the recombinations itself.

tbazilegith commented 11 months ago

Thanks!

From: nickjcroucher @.> Sent: Thursday, August 3, 2023 2:41 AM To: nickjcroucher/gubbins @.> Cc: Tassy Bazile @.>; Author @.> Subject: Re: [nickjcroucher/gubbins] alignment to use in final tree (Issue #380)

It uses the original input alignment, the script will mask the recombinations itself.

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