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.
Program is actually available in versions 1.1.1 and 1.3.0
snapp -> snapp-1.1.1 snapp-1.1.1 snapp-1.3.0
Initialize environment by command
module add snapp-1.1.1
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
module add snapp-1.3.0 snapp-1.3.0 -help
Documentation is available in https://www.beast2.org/snapp/#Documentation, or in file /software/snapp-1.1.1/doc/SNAPP.pdf.