ben stöver ws 2013/2014 maximum parsimony with mega and paup* molecular phylogenetics – exercise
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Ben Stöver WS 2013/2014
Maximum parsimony with MEGA and PAUP*
Molecular Phylogenetics – exercise
Ben Stöver
Maximum parsimony with MEGA and PAUP*
Fortgeschrittenenmodul Molecular Phylogenetics
Winter term 2013/2014
11.02.2014
1.1 MP tree search in MEGA1. MEGA 2
• An alignment in MEGA format will be needed.
Ben Stöver
Maximum parsimony with MEGA and PAUP*
Fortgeschrittenenmodul Molecular Phylogenetics
Winter term 2013/2014
11.02.2014
1.2 MP parameters in MEGA
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• Pairwise deletion of gaps not possible, because MP works with a MSA and not with pairwise distances.
• „Test of phylogeny“ can be e.g. bootsrapping
• MP search method:• „Max-mini branch-and-
bound“ is the branch-and-bound implementation of MEGA.
• Close-Neighbor-Interchange is a branch swapping algorithm (heuristic search)
• See the help for detailed information an all features
1. MEGA
Ben Stöver
Maximum parsimony with MEGA and PAUP*
Fortgeschrittenenmodul Molecular Phylogenetics
Winter term 2013/2014
11.02.2014
2.1 Using PAUP*2. PAUP* 4
• Phylogeny analysis using parsimony
(* and other methods)
• PAUP* is used by specifying commands in the PAUP* command line in a PAUP-block of a NEXUS file.
• By typing „?“ you get the list of commands.• „<command> ?“ displays the
available parameters for a command.
• When starting the program you can initially open a NEXUS file with your data (e.g. your alignment).
Ben Stöver
Maximum parsimony with MEGA and PAUP*
Fortgeschrittenenmodul Molecular Phylogenetics
Winter term 2013/2014
11.02.2014
2.2 PAUP* commands for tree searching
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• AllTrees: Performs a complete tree search (not more than 12 taxa possible).
• BandB: Performs a complete branch and bound search (not many taxa).
• HSearch: Performs a heuristic search with different methods.• Swap: Determines the branch-swapping algorithm. (TBR is
default.)• Start: The start tree to be used.
(STEPWISE|NJ|CURRENT|tree-number)• MulTrees: Specifies if all optimal trees or only one shall be
saved.• Set: Specifies the search criterion used by the other
commands (e.g. criterion=parsimony).
• ShowTrees: Shows all trees in memory on the command line.• SaveTrees: Saves the tree(s) in memory to a file
• BrLens: Determines weather to stare branch lengths (not with parsimony)
• File: The path to the output tree file
• Further information can be found by typing „<command> ?“ or in the PAUP* manual under „Downloads\information\PAUP“ in the course folder.
2. PAUP*