Question

I am trying to generate tree with fasta file input and Alignment with MuscleCommandline

import sys,os, subprocess
from Bio import AlignIO
from Bio.Align.Applications import MuscleCommandline
cline = MuscleCommandline(input="c:\Python26\opuntia.fasta")
child= subprocess.Popen(str(cline),
                         stdout = subprocess.PIPE,
                         stderr=subprocess.PIPE,
                        shell=(sys.platform!="win32"))
align=AlignIO.read(child.stdout,"fasta")
outfile=open('c:\Python26\opuntia.phy','w')
AlignIO.write([align],outfile,'phylip')
outfile.close()

I always encounter with these problems

Traceback (most recent call last):
  File "<string>", line 244, in run_nodebug
  File "C:\Python26\muscleIO.py", line 11, in <module>
    align=AlignIO.read(child.stdout,"fasta")
  File "C:\Python26\Lib\site-packages\Bio\AlignIO\__init__.py", line 423, in read
    raise ValueError("No records found in handle")
ValueError: No records found in handle

Answer 1

Biopython 1.54 was released today with a stable version of the Bio.Phylo module. I’ve updated the documentation with an example pipeline for generating trees. For simplicity, the example uses ClustalW to align sequences and generate a tree, instead of Muscle and Phylip, but most of the code is still the same or similar.

http://biopython.org/wiki/Phylo#Example_pipeline

If you’ve already generated a tree with Phylip (using the .phy alignment as input), you can still follow the Phylo examples in general. Phylip creates a Newick file with a name like “outttree” or “foo.tree”.

(Feel free to merge this with Brad’s answer; I can’t write a comment in that thread yet.)