1. Ben Stöver WS 2013/2014 Maximum parsimony with MEGA and PAUP* Molecular Phylogenetics – exercise

2. Ben Stöver Maximum parsimony with MEGA and PAUP* Fortgeschrittenenmodul Molecular Phylogenetics Winter term 2013/2014 11.02.2014 1.1 MP tree search in MEGA 1. MEGA 2 An alignment in MEGA format will be needed.

3. Ben Stöver Maximum parsimony with MEGA and PAUP* Fortgeschrittenenmodul Molecular Phylogenetics Winter term 2013/2014 11.02.2014 1.2 MP parameters in MEGA 3 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

4. 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. „ ?“ 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).

5. 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 5 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 „ ?“ or in the PAUP* manual under „Downloads\information\PAUP“ in the course folder. 2. PAUP*