MaxiPhi Code
Status: Alpha
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MaxiPhi
MaxiPhi is free software for the comparison of the diversity in viral metagenomes
by performing Monte-Carlo simulations. Its input is cross-contig spectra and the
output is beta-diversity plots representing the percent of genotypes shared and
permuted in abundance. Details on how MaxiPhi works are available in this paper:
Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, et al. (2006) The Marine
Viromes of Four Oceanic Regions. PLoS Biol 4(11): e368
http://dx.doi.org/10.1371/journal.pbio.0040368
To calculate beta-diversity you'll need cross-contig spectra computed by
Circonspect (http://sourceforge.net/projects/circonspect/) and estimates of
average genome length. See GAAS (http://sourceforge.net/projects/gaas/) to get
an estimate.
INSTALLATION
Put the MaxiPhi folder in the desired destination folder and open this folder. Then:
* Method A: Octave 3.4
Install version 3.4 of Octave (released in February 2011) or later (http://www.gnu.org/software/octave/).
Install GNUPlot as well if you want to be able to create graphs (http://www.gnuplot.info/).
* Method B: Octave and Octave-forge
You'll need to install Octave >= 3.0.1 (package octave-3.0 on GNU/Linux Debian) and its devel package (octave3.0-headers on GNU/Linux Debian). See http://www.gnu.org/software/octave/
Then download the following Octave-Forge packages:
- miscellaneous (>=1.0.0)
http://downloads.sourceforge.net/octave/miscellaneous-1.0.9.tar.gz?download
- optim (>=1.0.4)
http://downloads.sourceforge.net/octave/optim-1.0.12.tar.gz?download
Install the packages in the order you downloaded them by running:
octave --eval "pkg install miscellaneous-1.0.9.tar.gz optim-1.0.12.tar.gz"
Install GNUPlot as well if you want to be able to output graphs (http://www.gnuplot.info/).
* Method C: Matlab and optimization toolbox
Install Matlab 2006 or newer and its Optimization toolbox.
Now register the location of the current MaxiPhi folder. Open Octave/Matlab and
run the following (substituting by the appropriate value for your system):
addpath(genpath('/path/to/maxiphi/dir')); savepath();
This command adds the Maxiphi scripts to Octave/Matlab's search path. But before
this step, if you have a previous version of Maxiphi installed in a different
location, you have to remove it first and update the Octave/Matlab path:
rmpath(genpath('/path/to/old/maxiphi/dir')); savepath();
RUNNING MAXIPHI
In Octave or Matlab, try the commands below.
The MaxiPhi help explains the parameter taken by the maxiphi() function:
help maxiphi
Example for using a simple cross-contig spectrum (metagenome A against metagenome B):
maxiphi( {'A_vs_B.csp'} )
Same thing but specify in which folder the results should be written, which
rank-abundance model to use (powerlaw or logarithmic), and the average genome
length to assume:
maxiphi( {'A_vs_B.csp'}, 'results', 'logarithmic', [44000] )
Use control contig spectra (metagenome A against A and B against B) to increase
the accuracy of the beta-diversity estimates. This causes the computation to be
much longer because different average genome lengths are tested around the
specified average genome lengths:
maxiphi( {'A_vs_B.csp', 'A_vs_A.csp', 'B_vs_B.csp'}, 'results', 'logarithmic', [44000, 48000, 42000] )
Use the genome_length_delta, genome_length_mode and nof_intermediary_lengths to
control how many genome sizes to use and how different from the specified
average genome length (see 'help maxiphi' for full details):
maxiphi( {'A_vs_B.csp', 'A_vs_A.csp', 'B_vs_B.csp'}, 'results', 'logarithmic', [44000, 48000, 42000], 30, 'range', 101)
Now, if you're happy with the default parameters for the optimization of the
average genome length but need to change the number of permutations of the
Monte-Carlo simulation. For example if is it taking too much memory, decrease
it. Or if the control plots do not display nice contours, you will need to
increase it:
maxiphi( {'A_vs_B.csp', 'A_vs_A.csp', 'B_vs_B.csp'}, 'results', 'logarithmic', [44000, 48000, 42000], [], [], [], 400, 400, 200, 200)
To use MaxiPhi in a non-interactive way, try this in a terminal:
octave --silent --traditional --eval "maxiphi( <snip> ); exit;"
or:
matlab -nodesktop -nodisplay -nosplash -r "maxiphi( <snip> ); exit;"
COPYRIGHT AND LICENSE
MaxiPhi is copyright Florent Angly <florent.angly@gmail.com>, 2010
Contributions from Ben Felts and Steve Rayhawk.
MaxiPhi is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License (GPL) as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
MaxiPhi is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with MaxiPhi. If not, see <http://www.gnu.org/licenses/>.
