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SNAP Workbench Version 2.0

SNAP Workbench is a Java program that manages and coordinates a series of analysis programs for making inferences on population processes. SNAP workbench allows the user to customize the implementation of complex console programs and functions for the purpose of automating and enhancing data exploration. In our implementation, the workbench facilitates population parameter estimation by ensuring that the assumptions and program limitations of each analysis method are met and by providing a step-by-step methodology to effectively integrate both summary-statistic methods and coalescent-based population genetic models.

The workbench is programmed in Java to preserve platform independence across multiple operating systems. The program modules integrated in the workbench are written in C or Java and are available on a variety of computing platforms. The latest versions of the workbench for Mac OS X, Windows and Linux can be downloaded here.

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• How to cite SNAP Workbench

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How To Cite SNAP Workbench

References

Price, E.W., and I. Carbone. 2005. SNAP: workbench management tool for evolutionary population genetic analysis. Bioinformatics 21:402-404.

Aylor, D. L., Price, E.W. and I. Carbone. 2006. SNAP: Combine and Map modules for multilocus population genetic analysis. Bioinformatics 22:1399-1401.

Also, don't forget to cite the references for the separate program modules that you use in the workbench, as shown below.

How To Cite Program Modules in SNAP Workbench

clustalW

J. D. Thompson, D.G. Higgins, and T. J. Gibson
ftp://ftp.bio.indiana.edu/molbio/align/clustal/ (Mac OS X)
http://www.mirror.ac.uk (Windows)

Thompson, J. D., D. G. Higgins and T. J. Gibson, 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nuc. Acids Res. 22: 4673-4680.

genetree, seq2tr, treepic

R. C. Griffiths
http://www.stats.ox.ac.uk/~griff/software.html

Griffiths, R. C., and S. Tavaré, 1994 Ancestral inference in population genetics. Stat. Sci. 9: 307-319.

Bahlo, M., and R. C. Griffiths, 2000 Inference from gene trees in a subdivided population. Theor. Pop. Biol. 57: 79-95.

recom58

R. C. Griffiths
mailto:griff@stats.ox.ac.uk

Griffiths, R., and P. Marjoram, 1996 Ancestral inference from samples of DNA sequences with recombination. J. Comp. Biol. 3: 479-502.

RecMin

S. Myers
http://www.stats.ox.ac.uk/~myers/

Myers, S. R., and R. C. Griffiths, 2003 Bounds on the minimum number of recombination events in a sample history. Genetics 163: 375-394.

MDIV

R. Nielsen
mailto:rn28@cornell.edu

Nielsen, R., and J. Wakeley, 2001 Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158: 885-896.

Migrate

P. Beerli
http://evolution.genetics.washington.edu/lamarc/migrate.html

Beerli, P., and J. Felsenstein, 1999 Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152: 763-773

Beerli, P., and J. Felsenstein, 2001 Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. USA 98: 4563-4568.

RecPars

K. Fisker
http://www.daimi.au.dk/~compbio/recpars/

Hein, J., 1990 Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci. 98: 185-200.

seqtomatrix and permtest

R. Hudson
http://home.uchicago.edu/~rhudson1/source/permtest.html

Hudson, R. R., D. D. Boos and N. L. Kaplan, 1992a A statistical test for detecting geographic subdivision. Mol. Biol. Evol. 9: 138-151.

Hudson, R. R., M. Slatkin and W. P. Maddison, 1992b Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.

Treeview

Rod Page
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358.

gnuplot

ftp://ftp.gnuplot.info/pub/gnuplot/

ghostscript

http://www.cs.wisc.edu/~ghost/

ghostview

http://www.cs.wisc.edu/~ghost/

Combine and Map
http://snap.cifr.ncsu.edu

Aylor, D. L., Price, E.W. and I. Carbone. 2006. SNAP: Combine and Map modules for multilocus population genetic analysis. Bioinformatics 22:1399-1401.

Clade and Matrix

Bowden, L. C., Price, E.W. and I. Carbone
http://snap.cifr.ncsu.edu

Bowden, L. C., Price, E.W. and I. Carbone, 2008 SNAP Clade and Matrix, Version 2. Distributed over the Internet, http://www.cals.ncsu.edu/plantpath/faculty/carbone/home.html, Department of Plant Pathology, North Carolina State University.

Bremer*

Bowden, L. C. and I. Carbone
http://snap.cifr.ncsu.edu

Bowden, L. C. and I. Carbone, 2008 SNAP Bremer. Distributed over the Internet, http://www.cals.ncsu.edu/plantpath/faculty/carbone/home.html, Department of Plant Pathology, North Carolina State University.

*Requires PAUP* which can be purchased from:

http://paup.csit.fsu.edu/

Swofford DL (1998) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0. Sinauer Associates, Sunderland, Massachusetts.

pars and consense

http://evolution.genetics.washington.edu/phylip.html

Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.

beagle and kwarg (Section 26)

http://www.stats.ox.ac.uk/~lyngsoe/section26/

Lyngsø RB, Song YS, Hein J (2005) Minimum recombination histories by branch and bound. Proceedings of the 5th International Workshop on Algorithms in Bioinformatics (Lecture Notes in Bioinformatics 3692), 239-250.

HapBound and SHRUB

http://www.eecs.berkeley.edu/~yss/lu.html

Song YS, Wu Y, Gusfield D (2005) Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. Bioinformatics 21 Suppl 1, i413-i422.

Last Updated: 2/2/08