How to show bootstrap values on a phylogenetic tree constructed with RAxML I apologize for this very basic question. With @Michael G.'s help, I have been learning how to use RAxML to build a phylogenetic tree (How to define an outgroup to build a robust amino acid tree) and after running my analysis I obtained several results files. I have both a RAxML_bestTree.result file and a RAxML_bootstrap.result file. How do I "combine" these files so that my tree shows the bootstrap values? 

Any help will be greatly appreciated.
Depending on the search parameter settings RAxML produces several output files among which you normally find:


  RAxML_bipartitions.result: If you used the ­-f b option, this file
  will contain the input tree with confidence values from 0 to 100 drawn
  on its nodes! It is also printed when -f a ­x have been specified, at
  the end of the analysis the program will draw the BS support values on
  the best tree found during the ML search.
  
  RAxML_bipartitionsBranchLabels.result: Contains the same information
  as the file above, but support values are correctly displayed as
  Newick branch labels and not node labels! Support values always refer
  to branches/splits of trees and never to nodes of the tree. Note that,
  some tree viewers have problems displaying branch labels, they are
  however part of the standard Newick format.


from https://cme.h-its.org/exelixis/resource/download/NewManual.pdf

If you don't find the files in your output directory you did not specify the above parameters. If a rerun is not feasible you could you use the multinewick file RAxML_bootstrap.result with raxml or as input for the program splitstree to generate a consenus tree with different rules (majority rule, strict, etc.). However, these options don't guarantee to generate the topology of the maximum likelihood tree.