Question: RAxML outputs: which one I have to take ?
0
gravatar for Picasa
4.2 years ago by
Picasa590
Picasa590 wrote:

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 • 7.2k views
ADD COMMENTlink modified 4.1 years ago by Michael Dondrup48k • written 4.2 years ago by Picasa590
2
gravatar for Michael Dondrup
4.1 years ago by
Bergen, Norway
Michael Dondrup48k wrote:

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.

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Michael Dondrup48k

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 ?

ADD REPLYlink written 8 months ago by Picasa590
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