Some nodes have a bootstrap value of zero; what does it mean? Can I increase number of bootstrap replicates?
Phytobacteriology-UPNA opened this issue · 1 comments
I am analyzing 59 genomes of very closely related bacteria. Probably because I'm using draft genomes, I get only a 72% of the reference covered by the alignment. Anyway, some of the branches of the resulting phylogenetic tree get a zero or 1 as bootstrap value. Can you help me with any explanation of how can this be? I uploaded a typical tree I get (in newick format)
Also, is there any way to instruct Parsnp to construct the tree using more than 100 bootstrap replicates?
Thanks for the help!
Apologies for the late response. In this case, I think you are best off running Parsnp without the phylogeny step with --skip-phylogeny. Then, you can use the parsnp.snps.mblocks file in your output directory to generate the phylogeny using whichever tool/parameters you'd like.