Visualize Raxml 8 Bootstrap Tree

6.3 years ago by

jhc • 2.8k

Spain

jhc • 2.8k wrote:

Three quick solutions:

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

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

ADD COMMENT • link written 6.3 years ago by jhc • 2.8k

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.

ADD REPLY • link written 6.3 years ago by SES ♦ 8.3k

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

ADD REPLY • link written 5.4 years ago by kmkocot • 0

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