SNAPP
Description
SNAPP (SNP and AFLP Package for Phylogenetic analysis) is package for inferring species trees and species demographics from independent (unlinked) biallelic markers such as well spaced SNPs. It implements a full coalescent model, but uses a novel algorithm to integrate over all possible gene trees, rather than sampling them explicitly.
Like BEAST, a SNAPP analysis is controlled using a specially formatted XML file. This file can be created from scratch, or by using the graphical user interface in BEAUTi. SNAPP can be run directly from inside BEAUTi, or you can take the xml file and use it to run SNAPP on any computer or server.
Like BEAST and MrBayes, SNAPP does not output a single tree. Rather, it uses Markov chain Monte Carlo (MCMC) to generate multiple trees (and corresponding parameter values), each of which is a sample from the posterior distribution of species trees and parameters. The trees and parameter values are output as two files. As with all MCMC analyses, care must be taken when interpreting these outputs. For example, it is necessary to check convergence and be prepared to consider multiple plausible species trees, instead of just one. The file containing parameter values can be analysed using the Tracer software. As with all MCMC software, it is advisable to run multiple analyses, possibly tweaking proposal parameters, to validate an analysis.
License
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of snapp and load default version of snapp as
module avail snapp/ # list available modules module load snapp # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail snapp
and choose explicit version you want to use. This makes available the system variable $SNAPP which points to home directory of application. Also it makes available the module jdkibm-7 so the JAVA platform can be used. Example of work:
$ snapp -help
Usage: snapp [-window] [-options] [-working] [-seed] [-prefix <PREFIX>] [-overwrite] [-resume] [-errors <i>] [-threads <i>] [-help] [<input-file-name>]
-window Provide a console window
-options Display an options dialog
-working Change working directory to input files directory
-seed Specify a random number generator seed
-prefix Specify a prefix for all output log filenames
-overwrite Allow overwriting of log files
-resume Allow appending of log files
-errors Specify maximum number of numerical errors before stopping
-threads The number of computational threads to use (default auto)
-help Print this information and stop
Example: snapp test.xml
Example: snapp -window test.xml
Example: snapp -help
or
module add snapp-1.3.0
snapp-1.3.0 -help
Notice: This application use or needs GUI – graphical interface. To use the application in graphical mode see Remote desktop or X-Window.
Documentation
Documentation is available in https://www.beast2.org/snapp/#Documentation, or in file /software/snapp-1.3.0/doc/SNAPP.pdf.