SATè - S imultaneous A lignmnent and T ree E stimation

About SATè

SATè is a software package to infer sequence alignment and phylogenetic tree simultaneously, combinding the power of popular alignment and tree inference programs.

The original algorithm was developed in Tandy Warnow 's group and described in a recent paper of Liu et al , please go to Kevin Liu's web page for more information.

In our implmentation, we used recursive CT-1 instead of CT-5 decomposition described in Liu et al . The supported external tools are:

ClustalW2 , MAFFT , MUSCLE , OPAL , PRANK , RAxML

Download and Installation (newest updates as of 03/30/2010)

SATè runs on three platforms, including Microsoft Windows, Mac OS X and Linux.

Programs with simple GUI are provided for Windows and OS X users, only command-line version is available on Linux.

• Microsoft Windows

Install Microsoft Visual C++ 2008 Redistributable Package (it is free), if you do not have it.

Download SATè for Windows here and unzip the package to your favorite directory. Double click run_sate_gui.exe to start the program.

• Mac OS X

Download SATè for OS X here and mount the downloaded disk image, drag SATè into your /Application folder. Double click SATe to run it.

Note: SATè has been tested on 10.4.11 and 10.5.8 and it works fine. For version older than 10.3, no tests have been done by us.

• Linux

Install Python 2.6 and Dendropy , if you do not have them.

Download SATè source code here and unzip the tar ball to your favorite directory.

The external alignment and tree inference tools have been pre-compiled on Ubuntu 8.04 and come with the SATè package.

Usage

• GUI version

The options are fairly straightforward. Please refer to Liu et al . for terminologies

Note : If you want to use OPAL alignment merger in SATè, Java should be installed and at least 2GB memory is needed.

• Command-line version

First-time user of SATè could try following command to get a feeling of its command-line version.

python run_sate. py -i test data/small. fasta -t test data/small. tree -j test

For all the command-line options and help information, please use

python run_sate. py -h

Advanced users may want to try more options with the configuration file, one example is shown here.

[clustalw2]
# specify the location of ClustalW2 alignment program
path = /home/jiaye/Projects/msaml/sate/bin/clustalw2	
 
[mafft]
path = /home/jiaye/Projects/msaml/sate/bin/mafft        
 
[muscle]
path = /home/jiaye/Projects/msaml/sate/bin/muscle      
 
[opal]
path = /home/jiaye/Projects/msaml/sate/bin/opal.jar
 
[prank]
path = /home/jiaye/Projects/msaml/sate/bin/prank
 
[raxml]
path = /home/jiaye/Projects/msaml/sate/bin/raxml
 
[sate]
# time-based stopping rule, unit in seconds
time_limit = 86400
 
# the size of largest subproblems
max_subproblem_size = 0.2				
 
# specify which alignment program to use for subproblems
aligner = mafft	                			
 
# specify which alignment merger program to use
merger = muscle                
 
# specify which tree inference program to use
tree_estimator = raxml
 
# specify how many CPUs available
num_cpus = 2					
 
# how the guide tree should be partitioned
break_strategy = centroid				

License

This implementation of SATè is distributed under the GPL license. The external tools included in SATè package have their own licenses.

Status

At this time, we are still actively adding functions and making changes to SATè.

The GIT repository is available here , we do not provide support for SATè obtained through GIT.

Contacts

If you have any questions about SATè or would like to be spammed about our recent progress, please contact us .

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Copyright © 2009 - 2010. Jiaye Yu and Mark Holder , University of Kansas