text: user5116: 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.
  
  user257: 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.
  
  user3848: Apologies for the delay. The calculation is a majority consensus phylogeny of a maximum likelihood bootstrap, which is superimposed into a maximum likelihood phylogram. That's the tech. speak over ... the command is,
  raxmlHPC -f b -m PROTGAMMAILG -n output_bootstrap.tre -t RAxML_bestTree* -z RAxML_bootstrap.result
  
  
  RAxML_bestTree* = your maximum likelihood tree without bootstraps (file is probably 1 line long)
  RAxML_bootstrap.result = your complete list of bootstraps (file is 500 lines long [or the number of bootstraps you set])
  output_bootstap.tre = final result tree,  i.e. majority consensus. This file is one line long but will have with all bootstraps attached to each branch.
  
  The calculation will take less than one minute. The code is C and very slick. Note the "RAxML_bestTree*" is probably better to write the file name in full, not truncated via the glob (*). BTW you must specify the model.
  Visualising the tree You use a Mac ... so the cool tree program is figtree . Make sure when you load it you click the branch option and set it to see your bootstraps, otherwise it will not visualise them by default. You might need to re-root the tree, from memory your command specified an outgroup. It might not be the right one though and figtree will easily re-root it for you. Bootstrap values above 75% are considered robust. If you get stuck, can chat but I'm not around until this time next week (bereavement leave and loads of meetings).
  
original_text: 5116: <p>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 (<a href="https://bioinformatics.stackexchange.com/questions/10534/how-to-define-an-outgroup-to-build-a-robust-amino-acid-tree">How to define an outgroup to build a robust amino acid tree</a>) and after running my analysis I obtained several results files. I have both a <em>RAxML_bestTree.result</em> file and a <em>RAxML_bootstrap.result</em> file. How do I "combine" these files so that my tree shows the bootstrap values? </p>
  
  <p>Any help will be greatly appreciated.</p>
   257: <p>Depending on the search parameter settings RAxML produces several output files among which you normally find:</p>
  
  <blockquote>
    <p><strong>RAxML_bipartitions.result</strong>: 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.</p>
    
    <p><strong>RAxML_bipartitionsBranchLabels.result</strong>: 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.</p>
  </blockquote>
  
  <p>from <a href="https://cme.h-its.org/exelixis/resource/download/NewManual.pdf" rel="nofollow noreferrer">https://cme.h-its.org/exelixis/resource/download/NewManual.pdf</a></p>
  
  <p>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.</p>
   3848: <p>Apologies for the delay. The calculation is a majority consensus phylogeny of a maximum likelihood bootstrap, which is superimposed into a maximum likelihood phylogram. That's the tech. speak over ... the command is,</p>
  
  <pre><code>raxmlHPC -f b -m PROTGAMMAILG -n output_bootstrap.tre -t RAxML_bestTree* -z RAxML_bootstrap.result
  </code></pre>
  
  <ul>
  <li>RAxML_bestTree* = your maximum likelihood tree without bootstraps (file is probably 1 line long)</li>
  <li>RAxML_bootstrap.result = your complete list of bootstraps (file is 500 lines long [or the number of bootstraps you set])</li>
  <li>output_bootstap.tre = final result tree,  i.e. majority consensus. This file is one line long but will have with all bootstraps attached to each branch.</li>
  </ul>
  
  <p>The calculation will take less than one minute. The code is C and very slick. Note the "RAxML_bestTree*" is probably better to write the file name in full, not truncated via the glob (*). BTW you must specify the model.</p>
  
  <p><strong>Visualising the tree</strong> You use a Mac ... so the cool tree program is <a href="http://tree.bio.ed.ac.uk/software/figtree/" rel="nofollow noreferrer">figtree</a> . Make sure when you load it you click the branch option and set it to see your bootstraps, otherwise it will not visualise them by default. You might need to re-root the tree, from memory your command specified an outgroup. It might not be the right one though and figtree will easily re-root it for you. Bootstrap values above 75% are considered robust. If you get stuck, can chat but I'm not around until this time next week (bereavement leave and loads of meetings).</p>
  