187Other Algorithms
WhilegreedyalgorithmsandIParegeneralstrategiesforallProblems1–5,other
algorithmshavebeenappliedtosolvespecialcases.Forexample,simulatedanneal-
ingalgorithms(Possinghametal. 2000 ) were introduced to solve the reserve selec-
tionProblems 4 and 5 underspeciesrichnesswithanopportunitytominimizethe
connectivity between the areas such as the boundary lengths. Dynamic program-
mingalgorithms(DPA)havebeenappliedtosolveProblem 2 underPD(Pardiand
Goldman 2007 ).DPAwasfurtherextendedtomaximizeSDoncircularsplitnet-
works (Minh et al. 2009a, b).Otherspecialtypesofsplitnetworkswereexploited
tosolveProblem 1 (Spillneretal. 2008 ; Bordewich et al. 2009 ).
Computer Software
Conservation planning software like Marxan (Ball et al. 2009 ) and Zonation
(Moilanen et al. 2009 ) mainly focus on species richness. However, both programs
canindirectlyaccountforphylogeneticdiversity(seealsoSilvano,Valdujoand
Colli, chapter “PrioritiesforConservationoftheEvolutionaryHistoryofAmphibians
in the Cerrado”and Arponenand Zupan,chapter “RepresentingHotspotsof
Evolutionary History in Systematic Conservation Planning for European
Mammals”).Onlyafewprogramsexplicitlyallowtocomputephylogeneticdiver-
sity (Webb et al. 2008 ; Kembel et al. 2010 ).Inthefollowingwedescribetwopro-
grams relevant for the SD analysis.
SplitsTree
SplitsTree (Huson and Bryant 2006 ) is a user-friendly and leading software to
reconstruct and visualize phylogenetic networks from multiple sequence alignments,
distance matrices, or sets of trees. SplitsTree implements a wide range of split net-
work inference methods such as split decomposition (Bandelt and Dress 1992b) and
neighbor-net (Bryant and Moulton 2004 ). SplisTree has a limited ability to compute
PDandSD.ItworksforallmajorplatformsincludingWindows,MacOSX,and
Unix.MoreinformationaboutSplitsTreeisavailableathttp://www.splitstree.org.
PDA: Phylogenetic Diversity Analyzer
PDA(Minhetal. 2009 )isasoftwaretoolthatcomputesandmaximizesspecies
richness,PD,andSDgivenavarietyofuser-definedconstraintsincludingbudget,
ecological,andgeographicalconstraints.PDAcanbeusedinconjunctionwith
SplitsTreetoworkwithSD.ItsolvesallProblems1–5bygreedyalgorithms,
Split Diversity: Measuring and Optimizing Biodiversity Using Split Networks