Friday, June 19, 2009

Install the Emboss versions of Phylip programs on Ubuntu

One day I will use this space to write something that might actually be of general interest. Today is not that day. I've spend really too much time this week compiling and recompiling the Emboss version of Phylip - Joe Felsenstein's suite of phylogenetic programs to run in Ubuntu. Born as I was into the age of precompiled packages rolling my own programs has always scared me a little bit, but in this case I found qo many pitfalls I thought the karmic thing to do would be adding the answer to the hive-mind:

You need the EMBOSS sources to compile the phylip programs so download the latest EMBOSS release (6.0.1) (ftp server)
unzip and unpack the files somewhere
If you want to use distance matrices you need a patch, 1.12, from here

from your emboss folder unpack the patch and apply it:

~/EMBOSS-6.0.1$ gunzip -c /..someplace../patch-1-12.gz | patch -p1

In order to compile emboss we need the source for libplplot which is avaliable as a package:
```
$sudo apt-get install libplplot-dev
```
Now you can compile emboss as per the INSTALL file, (usually make, make install)
Next the Phylip tools, download them here
Make a new directory within your emboss folder called 'embassy' - unpack/untar the files into it
Move into the the unpacked phylip folder, and follow the instructions in INSTALL (they suggest using autoconf which I did)

And that should be it, all the Phylip packages are now duplicated (with the nice emboss interface) with the emboss versions having a leading 'f' - so dnadist becomes fdnadist.

Posted by David Winter 11:59 AM