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Data-Display Networks

SplitsTreeHuson (1998); Huson, Bryant (2006)http://www.splitstree.org/
NetworkRöhl (1999)http://www.fluxus-engineering.com/sharenet.htm
ArlequinExcoffier, et al. (2005); Excoffier, Lischer (2010)http://cmpg.unibe.ch/software/arlequin35/
TCSClement, Posada, Crandall (2000)http://darwin.uvigo.es/software/tcs.html
T-RexMakarenkov (2001)http://www.trex.uqam.ca/
SpectroNetHuber, Langton, Penny, Moulton, Hendy (2002)http://www.massey.ac.nz/massey/fms/AWC/download/Spectronet127.exe
CombineTreesCassens, Mardulyn, Milinkovitch (2005)http://applications.lanevol.org/combineTrees/
PopARTLeigh, Bryant (2015)http://popart.otago.ac.nz/

Evolutionary Networks

Cluster and Triplet networks

CASSvan Iersel, Kelk, Rupp, Huson (2010a)http://sites.google.com/site/cassalgorithm/
DendroscopeHuson, Richter, Rausch, Dezulian, et al. (2007)http://dendroscope.org/
LEVEL2van Iersel, Keijsper, Kelk, Stougie, et al. (2009)http://skelk.sdf-eu.org/level2triplets.html
LEV1ATHANHuber, van Iersel, Kelk, Suchecki (2011)http://skelk.sdf-eu.org/lev1athan/
MARLONvan Iersel, Kelk (2011a)http://skelk.sdf-eu.org/marlon.html
SIMPLISTICvan Iersel, Kelk (2011a)http://skelk.sdf-eu.org/simplistic.html

Tree-based networks

EEEPBeiko, Hamilton (2006)http://acb.qfab.org/acb/eeep/
HorizStoryMacLeod, Charlebois, et al. (2005)Not currently available
HybridInterleaveCollins, Linz, Semple (2011)http://www.math.canterbury.ac.nz/~c.semple/software.shtml
HybridNETChen, Wang (2010)hhttp://www.cs.cityu.edu.hk/~lwang/software/Hn/treeComp.html
LatTransAddario-Berry, Hallett, Lagergren (2003)Not currently available
PhylonetThan, Ruths, Nakhleh (2008)ttp://bioinfo.cs.rice.edu/phylonet/
PIRNWu (2010)http://www.engr.uconn.edu/~ywu/PIRN.html
PrunierAbby, Tannier, Gouy, Daubin (2010)http://pbil.univ-lyon1.fr/software/prunier/
RIATA-HGTNakhleh, Ruths, Wang (2005a)http://bioinfo.cs.rice.edu/phylonet/
SPRDistWu (2009)http://www.engr.uconn.edu/~ywu/SPRDist.html
SPRITHill, Nordström, Thollesson, et al. (2010)http://code.google.com/p/phylogenetics/
TNTGoloboff (2007)http://www.zmuc.dk/public/Phylogeny/TNT/

Character networks (Recombination)

Beagle / KwargLyngsø, Song, Hein (2005)http://www.stats.ox.ac.uk/~lyngsoe/section26/
GalledTreeGusfield, Bansal, Bafna, Song (2007)http://wwwcsif.cs.ucdavis.edu/~gusfield/software.html
SHRUB, SHRUB-GCSong, Ding, Gusfield, Langley, Wu (2007)http://wwwcsif.cs.ucdavis.edu/~gusfield/software.html

Deep coalescence

BEASTHeled, Drummond (2010)http://beast.bio.ed.ac.uk/
BESTLiu (2008)http://www.stat.osu.edu/~dkp/BEST/introduction/
GeneTreePage (1998)http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html
PhybaseLiu, Yu (2009)http://faculty.franklin.uga.edu/lliu/content/phybase
PhylonetThan, Ruths, Nakhleh (2008)ttp://bioinfo.cs.rice.edu/phylonet/
STEMKubatko, Carstens, Knowles (2009)http://www.stat.osu.edu/~lkubatko/software/STEM/

Duplication–loss or Duplication–loss plus transfer

DupTreeWehe, Bansal, Burleigh, Eulenstein (2008)http://genome.cs.iastate.edu/CBL/DupTree/
GeneTreePage (1998)http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html
JaneConow, Fielder, Ovadia, Libeskind-Hadas (2010)http://www.cs.hmc.edu/~hadas/jane/
NotungChen, Durand, Farach-Colton (2000)http://goby.compbio.cs.cmu.edu/notung/
PrIME-GSRÅkerborg, Sennblad, Arvestad, Lagergren (2009)http://prime.sbc.su.se/primeGSR/
SoftparsmapBerglund-Sonnhammer, Steffansson, et al. (2006)http://www.ii.uib.no/~steffpar/softparsmap/
TarzanMerkle, Middendorf (2005)http://pacosy.informatik.uni-leipzig.de/pv/Software/Tarzan/PV-Tarzan.engl.html
TreeFitterRonquist (2002)http://sourceforge.net/projects/treefitter/
TreeMapCharleston (1998)http://rp-www.cs.usyd.edu.au/~mcharles/software/treemap/treemap.html
URecGórecki, Tiuryn (2007)http://bioputer.mimuw.edu.pl/~gorecki/urec/

Other methods

Bio-PhyloNetworkCardona, Rosselló, Valiente (2008a)http://dmi.uib.es/~gcardona/BioInfo/
NepalPark, Jin, Nakhleh (2010)http://old-bioinfo.cs.rice.edu/nepal/
PhylonetThan, Ruths, Nakhleh (2008)http://bioinfo.cs.rice.edu/phylonet/
PADRELott, Spillner, Huber, Moulton (2009)https://www.uea.ac.uk/computing/padre
RecParsHein (1993)http://www.daimi.au.dk/~compbio/recpars/recpars.html


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