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.