Finding the best tree
As was discussed last lecture, the problem of nding the most parsimonious
tree is NP-complete. This implies that we wont be able to nd the absolute
best tree for large numbers of species. At this point we have
Wednesday, March 24, 2004
All problems are of equal value.
1. In an unrooted ternary (or trichotomous) phylogenetic tree each of the
internal nodes has 4 neighbors.
(a) How many unrooted ternary phylogenetic trees are there with
Phenetic/Distance Methods for Reconstructing Phylogenetic Trees
Phenetics is based upon the intuitively appealing notion that organisms
within the same species exhibit more overall similarity than their similarity
with organisms in
Do parsimony methods always work?
As was pointed out earlier, distance methods like UPGMA fail to reconstruct
the correct phylogeny when the molecular clock hypothesis fails. Intuitively,
the reason is that when species evolve at d
Reliability of Inferred Trees
The correctness of the conclusions we draw from a phylogeny is predicated
upon having the true phylogeny of the species we are investigating. But different methods of tree inference often give dierent
What is an Algorithm?
An algorithm is a recipe, strategy, method, procedure, etc. Like a recipe
an algorithm takes inputs (ingredients) and follows a series of steps to produce an output (a gourmet meal). A recipe is the solution t
Maximum Parsimony Methods
Lets say we have three species a, b, and c for which we have measured a
single character. Assume a and b have the character and c doesnt. There
are 3 possible rooted trees for these 3 species. See Figure 1
All of the approaches to inferring phylogenies from sequence data we have
considered require that we have aligned the sequences. For distance methods we use the alignment to compute the distance between pairs of
Maximum likelihood methods
The last class of methods for inferring phylogenies we consider are called
maximum likelihood methods. Their introduction is most often attributed
to Felsenstein in the early 1980s though the idea of app