[BioPython] biopython

[Peter]

Michael Fahy wrote:
> If you run clustalw and pass it command line arguments it will
> automatically  write the guide tree to a file but I have not be
 > able to get it to write the other tree to a file.

If you use filename.fasta as input (or similar extensions), then by 
default Clustalw will call the alignment filename.aln and the guide tree 
filename.dnd (I normally accept these defaults myself).

An example of changing the alignment filename (tested on Linux):

clustalw -infile=demo.faa -outfile=demo.align

This will result in an alignment, demo.align (our specified name), and a 
guide tree called demo.dnd (default naming).

Another command line:

clustalw -infile=demo.faa -newtree=demo.tree

This will result only in a guide tree, demo.tree (our specified name), 
but no alignment.

I don't know if you can get clustal to output both the alignment and the 
guide tree specifying both filenames.

 > Is there consensus in the research community that , while clustalw
 > was a useful program for doing multiple alignments, it has been
 > surpassed by newer programs such as MUSCLE and T-Coffee?

My personal impression is that many Biologists are quite content with 
clustalw. If they are unhappy with an alignment then they might edit it 
by hand, or investigate other tools. There may be a link to the age of 
the researcher, or their computer skill ;)

 > If so, it would be useful to update BipPython and the BioPython
 > Tutorial and Cookbook to use these alternative programs.

I would keep the clustalw examples, as I think the program is still 
widely used and is a useful baseline. Its also available on all the main 
operating systems.

As MUSCLE is available on Linux, Mac and Windows, extending the tutorial 
to use it might be nice.  Ideally we would also want to add a MUSCLE 
command line wrapper to Biopython to make calling the program as easy as 
possible.

For T-Coffee, its not obvious if its cross platform, but I suspect its 
not available for Windows. Again, the same caveat applies - it would be 
best to have a Biopython command line wrapper for it before adding it to 
the tutorial.

If you are happy at the command line, and running command line tools 
from python, then these tools should read FASTA files and output at 
least one output format Biopython can read.

Peter