Visualize Raxml 8 Bootstrap Tree

Question

[Pappu]

I am trying to visualize the tree using ete2 and figtree. But the programs don't seem to understand the bootstrap value given in RAxML_bipartitionsBranchLabels.test as branch_len[bootstrap value] : 0.44849636763673333961[20]

Could you tell me how can I visualize the trees with support values?

Answer 1

[jhc]

Three quick solutions:

1. ETE comes with a command line script for quick tree visualization called 'ete2' that should be in your path. Try the --raxml option.

2. Convert raxml newick file into the the standard format using regular expressions. Something like this should work:

cat RAxML_bipartitionsBranchLabels.mytree
'(A:1, (B:1, (C, D):0.44849636763673333961[20]):0.44849636763673333961[20]);'

cat RAxML.bipartitions | perl -p -i -e 's/:(\d+\.\d+)\[(\d+)\]/$2:$1/g'
(A:1, (B:1, (C, D)20:0.44849636763673333961)20:0.44849636763673333961);

3. Latest versions of RAxML produce a newick file with the correct standard format. You should see something like RAxML_bipartitionsBranchLabels.mytree and RAxML_bipartitions.mytree. They are the same tree, and the former has the correct format

[SES]

Nice solution. Just for reference, you don't need cat in the second command, perl will take the file from stdin or as an argument.

[kmkocot]

I tried this but I'm still having trouble with ete2. Here's the script I'm using:

from ete2 import Tree, faces, AttrFace, TreeStyle
t1=Tree('/home/kmkocot/Desktop/ete_test/RAxML_bipartitions.Best_425', format=0)
ancestor = t1.get_common_ancestor("PCAU","DMEL","DPUL")
t1.set_outgroup(ancestor)
print t1
print
print "Entoprocta"
print t1.check_monophyly(["NLAP", "GEBO"], "name", ignore_missing=False)
print t1.support

and here's the output I'm getting:

      /-PCAU
   /-|
  |  |   /-SAME
  |   \-|
  |     |   /-DPUL
  |      \-|
  |         \-DMEL
  |
  |      /-SAGI
  |     |
  |     |         /-SMAN
  |   /-|      /-|
--|  |  |   /-|   \-TPIS
  |  |  |  |  |
  |  |  |  |   \-SMED
  |  |   \-|
  |  |     |      /-BPLI
  |  |     |   /-|
  |  |      \-|   \-ARIC
  |  |        |
  |  |         \-GPAR
  |  |
  |  |   /-BNER
  |  |  |
   \-|  |            /-LPEC
     |  |         /-|
     |  |        |   \-LVIV
     |  |      /-|
     |  |     |  |   /-PCER
     |  |     |   \-|
     |  |   /-|      \-BGRA
     |  |  |  |
     |  |  |  |   /-MEGA
     |  |  |   \-|
     |  |  |      \-MACR
     |  |  |
     |  |  |               /-GPYR
     |  |  |            /-|
      \-|  |           |   \-NANO
        |  |         /-|
        |  |        |  |   /-HPSI
        |  |        |   \-|
        |  |      /-|      \-LCAL
        |  |     |  |
        |  |     |  |   /-PVAN
        |  |     |   \-|
        |  |     |      \-PARC
        |  |     |
        |  |     |            /-PPER
        |  |     |         /-|
        |  |     |        |   \-MGRO
        |  |     |      /-|
        |  |     |     |  |   /-CMAR
        |  |   /-|     |  |  |
         \-|  |  |     |   \-|      /-LLON
           |  |  |     |     |   /-|
           |  |  |     |      \-|   \-LLAC
           |  |  |   /-|        |
           |  |  |  |  |         \-LRUB
           |  |  |  |  |
           |  |  |  |  |      /-CLIN
           |  |  |  |  |   /-|
           |  |  |  |  |  |   \-CHON
           |  |  |  |   \-|
           |  |  |  |     |   /-TPO1
           |  |   \-|      \-|
           |  |     |         \-TPO2
           |  |     |
           |  |     |   /-PAGA
           |  |     |  |
           |  |     |  |            /-PGOU
           |  |     |  |         /-|
           |  |     |  |        |   \-CTOR
           |  |      \-|      /-|
           |  |        |     |  |   /-HROB
           |  |        |     |   \-|
           |  |        |   /-|      \-CTEL
           |  |        |  |  |
            \-|        |  |  |   /-BPRO
              |         \-|   \-|
              |           |      \-PLAM
              |           |
              |           |   /-ASUC
              |            \-|
              |               \-GDIB
              |
              |            /-LASE
              |         /-|
              |      /-|   \-LRUG
              |     |  |
              |     |   \-ROLI
              |   /-|
              |  |  |      /-SCLE
              |  |  |   /-|
              |  |  |  |   \-PCAL
              |  |   \-|
              |  |     |   /-ACRA
              |  |      \-|
              |  |        |   /-NCAR
              |  |         \-|
              |  |            \-MSCH
              |  |
              |  |      /-LHYA
               \-|   /-|
                 |  |  |   /-OVUL
                 |  |   \-|
                 |  |     |   /-DGIG
                 |  |      \-|
                 |  |        |   /-SESC
                 |  |         \-|
                 |  |            \-SLES
                 |  |
                 |  |            /-SVEL
                 |  |         /-|
                 |  |        |   \-ETEN
                 |  |        |
                  \-|      /-|      /-VLIE
                    |     |  |   /-|
                    |     |  |  |   \-RPHI
                    |     |   \-|
                    |     |     |   /-MEDU
                    |   /-|      \-|
                    |  |  |        |   /-CGIG
                    |  |  |         \-|
                    |  |  |            \-PFUC
                    |  |  |
                    |  |   \-NPER
                    |  |
                    |  |         /-PPUL
                     \-|      /-|
                       |     |  |   /-LGIG
                       |     |   \-|
                       |   /-|      \-PVUL
                       |  |  |
                       |  |  |   /-HRUF
                       |  |   \-|
                       |  |     |   /-ACAL
                        \-|      \-|
                          |        |   /-NLAP
                          |         \-|
                          |            \-CFOR
                          |
                          |   /-GEBO
                           \-|
                             |   /-ETET
                              \-|
                                 \-GTOL

Entoprocta
(True, 'monophyletic')
Traceback (most recent call last):
  File "ete2_script.py", line 11, in <module>
    print t1.support("NLAP", "CFOR", "ACAL")
TypeError: 'float' object is not callable