Installation of lorax under linux can be done either directly via the 
virtualenv package or indirectly via Anaconda Python and packages in the
bioconda channel.  Which path you choose depends on your preferences.

Using a direct install (via virtualenv) gives you the most control over
what happens.  You may specify the directory you would like the virtual
environment to use, and you may control the building of the binaries.
Note that the FastTree binary is built by lorax at setup time; this
design choice was dictated by distrust of FastTree being built correctly
(with OpenMP and double-precision calculations enabled) on most platforms,
a problem made worse by the lack of configuration files for FastTree).
If you choose the direct option, you will have to make sure that the binaries
for HMMer3.1_beta2 and RAxML are installed correctly for your distribution,
as well as biopython and its dependencies. The advantage that comes with this
hassle is that quite a bit of computational time may be spent running those
binaries (particularly RAxML), so you may wish to build them from source to take
advantage of the processor features (e.g., AVX) specific to your machine.
If you choose the direct install route and if you use the Gentoo source
distribution, you may wish to take advantage
 of the ebuilds in the ebuilds/ directory are used for installation of lorax
under Gentoo.  They are intended to go in a local overlay under dev-python/.
If you will do a direct install, follow the directions in INSTALL.direct.txt.

If you are a casual user of lorax, installation from Anaconda Python will
get you up and running more quickly.  Follow the directions in 
INSTALL.anaconda.txt.
