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Introduction to Phylogenetic Networks

Datasets used in the Figures and Text

Book ref.

Source of data

Type of data

Data file

Figure 1.1Donoghue et al. (2004)tree from the paper
Figure 1.2see Fig. 1.1
Figure 1.3see Fig. 1.1nexus file for DendroscopeViburnum.nex
Figure 1.4Øines and Brännström (2011)nexus file for SplitsTreeDermanyssus.nex
Figure 1.5see Fig. 1.4
 
Figure 2.8Morrison (2005) nexus file for MacCladeVertebrates.nex
Figure 2.9Lemey et al. (2005)nexus file for PAUP*HIV1.nex
TextSanson et al. (2002)nexus file for PAUP*Sanson.nex
Figure 2.10Original datanexus file for MacCladeCrustacea.nex
Figure 2.11see Fig. 3.31
Figure 2.13Morrison (2007)nexus file for PAUP*Coccidia.nex
Figure 2.16Falush et al. (2003)tree from the paper
 
Figure 3.1Morrison et al. (2004)nexus file for PAUP*Toxoplasmatinae.nex
Figure 3.2O'Donnell et al. (2000)nexus file for SplitsTreeFusarium1.nex
Figure 3.3see Fig. 2.10
Figure 3.10Morrison et al. (2003)nexus file for MacCladeSarcoptes1.nex
Figure 3.11see Fig. 2.10
Figure 3.12Balakrishnan et al. (2003)nexus file for SplitsTreeCervisHaplotypes.nex
Figure 3.13Macaulay et al. (1999)network from the paper
Figure 3.14Balakrishnan et al. (2003)RDF file for NetworkCervisHaplotypes.rdf
Figure 3.16Gaur et al. (1992)nexus file for SplitsTreePrimates1.nex
Figure 3.17Jirku et al. (2009)nexus file for SplitsTreeGoussia.nex
Figure 3.19Troell et al. (2006)nexus file for SplitsTreeHaemonchus.nex
Figure 3.20Skerrat et al. (2002)nexus file for SplitsTreeSarcoptes2.nex
Figure 3.21Jondelius & Thollesson (1993)nexus file for SplitsTreeRhabdocoela.nex
Figure 3.24see Fig. 3.12
Figure 3.25Gross et al. (2003)nexus file for TCSHelianthus.nex
nexus file for CombineTreesHelianthus.tre
ARP file for ArlequinHelianthus.arp
RDF file for NetworkHelianthus.rdf
TextHöglund et al. (2004)nexus file for TCSDictyocaulus.nex
Figure 3.26Balakrishnan et al. (2003)nexus file for TCSCervis.nex
nexus file for CombineTreesCervis.tre
see also 3.12 & 3.14
Figure 3.27Su et al. (2001)Phylip filr for TCSPanda.phy
Figure 3.28Atchley & Fitch (1993)distance file for T-RexMice.txt
Figure 3.29Winchell et al. (2002)nexus file for SplitsTreeWinchell.tre
Figure 3.30Morrison (2006a)nexus file for SplitsTreeCryptosporidium.tre
Figure 3.31Bray et al. (2009)nexus file for MrBayesBrayProtein.nex
nexus file for MrBayesBrayRNA.nex
Figure 3.32see Fig. 3.31 & 3.33
Figure 3.33Bray et al. (2009)nexus file for MrBayesBrayCombined.nex
 
Figure 4.7Baroni et al. (2006)gene trees and network from the paper(taxon names from Lockhart)
Figure 4.17Baumel et al. (2002)trees from the paper
Figure 4.18Baumel et al. (2002)nexus file for DendroscopeSpartina.tre
triplet file for Lev1athanSpartinaTriplets1.txt
triplet file for SimplisticSpartinaTriplets2.txt
Figure 4.19Walton et al. (2004)nexus file for PAUP*SarcoptesCOI.nex
nexus file for PAUP*Sarcoptes16S.nex
Figure 4.20Morrison (2006a)nexus file for GeneTreeCryptosporidium.nex
Figure 4.21Kroken and Taylor (2001)binary file for GalledTreeLichen.txt
Figure 4.22Belfiore et al. (2008)nexus file for SplitsTreeGopherTrees.nex
xml file for BeastGopher.xml
Figure 4.23see Fig. A1.18
Figure 4.24see Fig. 3.20
Figure 4.25see Fig. 3.30
Figure 4.26Smedmark et al. (2005)newick file for PadreColurieae.tre
Figure 4.27Huber et al. (2011)trees from the paper
 
Figure 5.1Sousa et al. (2008)nexus file for SplitsTreeBacteriophage.nex
Figure 5.2Blanc et al. (2007)network from the paper
 
Figure A1.1Smith and Klein (1994)nexus file for SplitsTreePiceaFungi.nex
Figure A1.2Morrison (2005)nexus file for SplitsTreeToxoplasma.nex
Figure A1.3Pecher et al. (2004)nexus file for SplitsTreePerkinsus.nex
Figure A1.4Cooper et al. (2001)nexus file for SplitsTreeRatites.tre
Figure A1.5Morrison (2009a)nexus file for SplitsTreeGregarines.nex
Figure A1.6Pisani et al. (2004)nexus file for SplitsTreePisani.nex
Figure A1.7Holmdahl et al. (1999)nexus file for SplitsTreeSarcocystis1.nex
nexus file for SplitsTreeSarcocystis2.nex
Figure A1.8Willis et al. (1992)nexus file for SplitsTreeApis.nex
Figure A1.9Morrison (2007)nexus file for SplitsTreeCoccidia.tre
Figure A1.10Compilationnexus file for SplitsTreeMorphology.nex
Figure A1.11Weisburg et al. (1989)nexus file for SplitsTreeEubacteria.nex
Figure A1.12Brant and Ortí (2003)nexus file for SplitsTreeBlarina.nex
Figure A1.13Redenbach and Taylor (2002)nexus file for SplitsTreeSalvelinus.nex
Figure A1.14O'Donnell et al. (2000)nexus file for SplitsTreeFusarium2.nex
Figure A1.15Bapteste et al. (2005)nexus file for SplitsTreeAlphaproteobacteria.nex
Figure A1.16Rivera and Lake (2004)network from the paper
Figure A1.17O'hUigin et al. (2002)nexus file for SplitsTreePrimates2.nex
Figure A1.18Morrison (2005)nexus file for SplitsTreeToxoplasmatinae2.nex

Combined data files

Zip file of all datasets [307 KB]


http://www.rjr-productions.org/Networks/DataSets.html

Last updated Friday 20 January 2012 by


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