How to cite

 

SNAP Workbench papers to cite


 

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.

 

Program Modules in SNAP Workbench to cite


 

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://popgen.sc.fsu.edu/Migrate/Migrate-n.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

http://www.gnuplot.info/
 
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://snap.hpc.ncsu.edu/, 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://snap.hpc.ncsu.edu/, 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.