Resources
The list The Felsenstein's list.
Treebase.
Servers to run/draw trees
ClustalW/Phylip servers.
Probabilistic models.
Sequence polymorphims.
Phyloblast.
Phylodendron.
Programs
DualBrothers.
Bayesian.
MrBayesCOOL.
SSa Maximum likelihood.
AsaturA Deals with saturation in aa sequences.
PHASE For RNA secondary structures.
Phylip programs.
MEGA.
Tree Drawing tools
TreeViewSimple and easy.
TrePlot Plotter.
PhyloDraw.
a Perl script by Julian Gough.
BOSQUE.
NJ plot.
ATV Java based.
Perl scripts.
Examples of alignment formats
- An example of a Nexus format for
program Mr.Bayes
- Here a
TOOL To CONVERT FORMATS
Some exercises:
- Problem 0
- Run a phylogentic (NJ) analyses with 1000 bootstrap
replicates
- Runa a Minimum evolution analyses with 1000 bootstrap
replicates
- >>>>> ARE THEY DIFFERENT?
- Now:
- Change the default parameters to:
- p-distance first (then JTT matrix).
- rates to gamma (2.0 or 1.0).
- Change the gap option from complete to pairwise.
- RUN NJ and ME with bootstrap (1000).
- >>>>>>> How do these changes affect the outcome?
- problem 1
- Problem 2
- Pick from GeneBank at least a minimum of 8 orthologous sequences (Prot or DNA).
- Compute a good alignment.
- Run one distance-based method against a probabilistic method.
- Obtain bootstrap values for both methods.
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