How to convert tree in phylip format into newick format

Question

[arash.iranzadeh1980]

Hi,

Anyone knows How to convert tree in phylip format into newick format?

Thanks!

[neutrinoscientist]

 File "/home/x/.local/lib/python2.7/site-packages/Bio/AlignIO/__init__.py", line 234, in write
    raise ValueError("Unknown format '%s'" % format) ValueError: Unknown format 'newick'

any help?

[Joe]

I'd suggest opening a new question, but in any event, this shouldn't be posted as an answer here.

EDIT, the previous code I posted was untested so I've just noticed a couple of problems with it and updated it accordingly. It's tested and should work properly now.

[neutrinoscientist]

am so sorry for adding this as an answer. sorry its just in mistake.

its still give error.

Traceback (most recent call last):
  File "convert_trees.py", line 9, in <module>
    Phylo.convert(infile,intype, outfile, outtype)
  File "/home/x/.local/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 90, in convert
    return write(trees, out_file, out_format, **kwargs)
  File "/home/x/.local/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 81, in write
    n = getattr(supported_formats[format], 'write')(trees, fp, **kwargs)
  File "/home/x/.local/lib/python2.7/site-packages/Bio/Phylo/NewickIO.py", line 58, in write
    return Writer(trees).write(handle, plain=plain, **kwargs)
  File "/home/x/.local/lib/python2.7/site-packages/Bio/Phylo/NewickIO.py", line 251, in write
    for treestr in self.to_strings(**kwargs):
  File "/home/x/.local/lib/python2.7/site-packages/Bio/Phylo/NewickIO.py", line 285, in to_strings
    for tree in self.trees:
  File "/home/x/.local/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 51, in parse
    for tree in getattr(supported_formats[format], 'parse')(fp, **kwargs):
KeyError: 'phylip'

[Joe]

Please post the command you're using.

[neutrinoscientist]

  python convert_trees.py phyliptree.phy phylip mytree.nwk newick

[Joe]

Ah yeah I see the issue. My fault. The previous code should not have said 'phylip'. This is an alignment format not a tree format.

What file are you trying to convert?

[neutrinoscientist]

I have a tree in phylip format and i want to convert it to newick format

[Joe]

Are you certain of that? Can you post a snippet of the file you have?

From the BioPython.Phylo documentation:

The second argument to each function is the target format. Currently, the following formats are supported:

newick
nexus
nexml
phyloxml
cdao

Answer 1

[Joe]

Very easily with biopython (you will need to install it of course, if you haven't already):

Create the following script:

from Bio import Phylo
import sys

infile = sys.argv[1]
intype = sys.argv[2]
outfile = sys.argv[3]
outtype = sys.argv[4]

Phylo.convert(infile,intype, outfile, outtype)

then call it from the command line like so:

$ python convert_trees.py mytree.nx nexus mytree.nwk newick

[neutrinoscientist]

not working Traceback (most recent call last): File "convert_trees.py", line 9, in <module> Phylo.convert(infile,intype, outfile, outtype) File "/home/maria/.local/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 90, in convert return write(trees, out_file, out_format, kwargs) File "/home/maria/.local/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 81, in write n = getattr(supported_formats[format], 'write')(trees, fp, *kwargs) File "/home/maria/.local/lib/python2.7/site-packages/Bio/Phylo/NewickIO.py", line 58, in write return Writer(trees).write(handle, plain=plain, *kwargs) File "/home/maria/.local/lib/python2.7/site-packages/Bio/Phylo/NewickIO.py", line 251, in write for treestr in self.to_strings(kwargs): File "/home/maria/.local/lib/python2.7/site-packages/Bio/Phylo/NewickIO.py", line 285, in to_strings for tree in self.trees: File "/home/maria/.local/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 51, in parse for tree in getattr(supported_formats[format], 'parse')(fp, **kwargs): KeyError: 'phylip'