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Maximum parsimony with MEGA and PAUP* Molecular Phylogenetics – exercise

Maximum parsimony with MEGA and PAUP* Molecular Phylogenetics – exercise. 1.1 MP tree search in MEGA. An alignment in MEGA format will be needed. 1.2 MP parameters in MEGA.

cassandra-murphy
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Maximum parsimony with MEGA and PAUP* Molecular Phylogenetics – exercise

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  1. Maximum parsimonywith MEGA and PAUP*MolecularPhylogenetics – exercise

  2. 1. MEGA 1.1 MP treesearch in MEGA • An alignment in MEGA format will beneeded.

  3. 1. MEGA 1.2 MP parameters in MEGA • Pairwisedeletionofgaps not possible, because MP workswith a MSA and not withpairwisedistances. • „Test ofphylogeny“ canbe e.g. bootsrapping • MP searchmethod: • „Max-mini branch-and-bound“ isthebranch-and-boundimplementationof MEGA. • Close-Neighbor-Interchange is a branchswappingalgorithm (heuristicsearch) • See thehelpfordetailedinformation an all features

  4. 2. PAUP* 2.1 Using PAUP* • Phylogenyanalysisusingparsimony(*andothermethods) • Whenstartingtheprogramyoucaninitially open a NEXUS filewithyourdata (e.g. youralignment). • PAUP* isusedbyspecifyingcommands in the PAUP* commandline in a PAUP-block of a NEXUS file. • Bytyping „?“ yougetthelistofcommands. • „<command> ?“ displaystheavailableparametersfor a command.

  5. 2. PAUP* 2.2 PAUP* commandsfortreesearching • AllTrees: Performs a completetreesearch (not morethan 12 taxapossible). • BandB: Performs a completebranchandboundsearch (not manytaxa). • HSearch: Performs a heuristicsearchwith different methods. • Swap: Determinesthebranch-swappingalgorithm. (TBR isdefault.) • Start: The starttreetobeused. (STEPWISE|NJ|CURRENT|tree-number) • MulTrees: Specifiesif all optimal treesoronlyoneshallbesaved. • Set: Specifiesthesearchcriterionusedbytheothercommands (e.g. criterion=parsimony). • ShowTrees: Shows all trees in memory on thecommandline. • SaveTrees: Savesthetree(s) in memoryto a file • BrLens: Determinesweathertostarebranchlengths (not withparsimony) • File: The pathtotheoutputtreefile • Further informationcanbefoundbytyping „<command> ?“ or in the PAUP* manualunder„Downloads\information\PAUP“ in thecoursefolder.

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