1. Maximum parsimony with MEGA and PAUP
Maximum parsimony with MEGA and PAUP* Molecular Phylogenetics – exercise

2. 1.1 MP tree search in MEGA An alignment in MEGA format will be needed.

3. 1. MEGA
1.2 MP parameters in MEGA
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

4. 2. PAUP*
2.1 Using PAUP*
Phylogeny analysis using parsimony (* and other methods)
When starting the program you can initially open a NEXUS file with your data (e.g. your alignment).
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.

5. 2.2 PAUP* commands for tree searching
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.