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RAxML outputs: which one I have to take ?

Hi,

RAxML produces 3 kinds of output at then end.

  • Best-scoring ML tree

  • Best-scoring ML tree with support values

  • Best-scoring ML tree with support values as branch labels

I am a totally beginner in phylogenie. Could someone explain what are the differences and which one I have to take for analysis?

Thanks a lot.

raxml output
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updated by Michael Dondrup Michael Dondrup • written by Picasa Picasa

1 answer

RAxML should produce an output file like RAxML_bestTree[your run id assigned using -n]. You could use this file and open it in a Phylogenetic tree viewer like FigTree.

Best-scoring ML tree with support values written to: RAxML_bipartitions.[run id]

Best-scoring ML tree with support values as branch labels written to: RAxML_bipartitionsBranchLabels[run id]

What you use depends on what you need for your analysis. If you need branch support values and not only branch lengths, then you need to use one of the latter two trees. Further, this depends on the software you are using to analyse the tree, as e.g. FigTree does not understand the bipartitionsBranchLabels Newick format, but RAxML_bipartitions works.

It would be better if the output was also available in Nexus or PhyML format.

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written by Michael Dondrup Michael Dondrup

Hi @Michael,

Best-scoring ML tree with support values written to: RAxML_bipartitions.[run id] is bootstrap value ? I am interested in it, do you know how to display on figtree ?

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written by Picasa Picasa

Sorry for not answering this earlier. For completeness, yes in my understanding these are bootstrap support values. When you open the file in FigTree it will propose to read "label", just accept this dialog. You can display support values by enabling node labels in the menu on the left side of the window.

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written by Michael Dondrup Michael Dondrup

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