The puma branch length is negative when I checked the file.
clustalw_cline = ClustalwCommandline(clustalw_exe, infile="related_data_set_renamed.fasta", outfile="related_data_set_aligned.fasta", output='fasta', bootlabels='NODE', bootstrap=1000) assert os.path.isfile(clustalw_exe), "Clustal W executable missing" stdout, stderr = clustalw_cline() tree = Phylo.read("related_data_set_renamed.dnd", "newick") tree.root_at_midpoint() tree.ladderize(reverse=True) Phylo.draw(tree)
I would like to fix the negative branch length through code but I am not sure what to do. In addition, I would like to add bootstrap values to the node points but I am unable to see them. I am thinking about using Bio.Phylo.TreeConstruction and use DistanceCalculator and DistanceTreeCalculator to instead make bootstrap values but would like to know if the ClustalWCommandline can can do it.