[Primeusers] binary package for Ubuntu 11.10 (64-bit) is available for download

[Lars Arvestad]

I would like to add that this is a new version which is faster and avoids problems that several users have encountered: the dreaded "division with zero".

The division by zero occurs when a solution that is possible gets probability zero due to limitations in the implementation of our algorithm. An important feature in PrIME is our technique of discretizing the species tree and this has two effects. First, many species trees have some very short branches and our first version of primegsr did not ensure that every species branch actually had discretization points, i.e., points where you could position a duplication. Second, if the starting gene tree is far away from the true tree, a reconciliation with the species tree may involve ridiculous numbers of duplications on single branches in the species tree. Again, not having enough points to put those duplications on makes the gene tree have zero probability. 

In the new version of the program, we make sure to have a minimum number of discretization points. In fact, you can regulate this using options (see the program help using "-h"), but please note that this also affects the speed of the program. 

It is still a good idea to instruct prime to start with a specific gene tree to avoid the weird solutions that appear when the starting tree is randomized (default behavior right now).

Please let us know how the software worked for you!

	Best regards,
	Lars Arvestad





Feb 8, 2012 kl. 11:35 AM skrev Erik Sjölund:

> On the web page:
> 
> http://prime.sbc.su.se/binary_packages.html
> 
> you can now find a Deb package for Ubuntu 11.10 (64-bit).
> 
> To install it first run:
> 
> apt-get install libxml2 liblapack3gf libatlas3gf-base libgfortran3 
> libopenmpi1.3 libquadmath0 libstdc++6 libxerces-c3.1 zlib1g
> 
> and then run
> 
> dpkg -i PrIME-phylo-1.0.1-Linux.deb
> 
> Please give us feedback so we know how it works.
> cheers,
> Erik Sjölund
> 
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