[bio-tools] New versions of motility and paircomp.

[Titus Brown]

Hi all,

I've just released updates to paircomp and motility.

paircomp is my simple fixed-width-window/dotplot analysis code.

motility is my simple PWM/energy operator motif searching tool.

The paircomp functionality hasn't significantly changed with this
release, but the 3-way transitivity code now works properly (*ahem*) and
I have added a ton of tests.  Consider this a 1.0 alpha release,
although I think the docs still say 0.9.

I've added some features to motility that are (IMO) kinda cool.
Basically you can now generate a list of all sites that score
above/below a certain threshold, and for situations where that kind of
list is too big (e.g. 22-bp motifs), you can ask about the probability
that such a site is generated.  This lets you calculate the significance
of finding N sites under a specific threshold T, for example.

Both toolkits are written in C++ and have a complete Python interface.

Anyway, if you care at all, the docs for motility are at

	http://issola.caltech.edu/~t/motility/

and the docs for paircomp are at

	http://issola.caltech.edu/~t/paircomp.new/

---

You can get motility from the Cartwheel CVS, directory /motility/, and
paircomp is under the FamilyJewels CVS, directory /familyjewels/.  Both
projects are hosted on SourceForge.

Alternatively, you can download them from issola,

	http://issola.caltech.edu/~t/transfer/motility-0.6.tar.gz
	http://issola.caltech.edu/~t/transfer/paircomp-0.9.tar.gz

I'm hoping to do a 1.0 release of both of these toolkits soon.  I've
just got a few more automatic tests to set up...

Let me know if you have any problems.

cheers,
--titus