Perform maximum parsimony tree with bootsrapping with the option to save all the replicate trees

Question

[jlsovaz]

Hello,

I am trying to create maximum parsimony trees from different nexus files with bootstrapping option. The problem is I would want to save all the replicates (trees) of the bootstrap analysis (for example, if I set 500 replicates, I would want to get the 500 trees as well as the consensus tree with the support values). Is it possible with any program (paup, mpboot, phylip...)?

Thanks,

Jose

Answer 1

[Jean-Karim Heriche]

Check the R packages ape and and phangorn. Both have bootstrapping functions that return trees.