Notes 20100720 113343 CS 798 Mohommad's Project Talk

From SnOwy - Ed's Wiki Notebook

Study different objective functions

• branch lengths
• correct topologies
• accuracy
• if the sequences being studied are short, the distances cannot be measured very well
• objective function used: the known actual distance versus the guessed distance given the method
• multiplicative noise model
• assume in nature, error is proportional to distance

ROSE

• random model of sequence evolution
• implements a probabilistic model of the evolution of sequences
• returns correct phylogeny and MSA
• old -- classic, still used

Noise independent of topology?

• additive noise model
• internal nodes manage to retain the noise of its child taxa
• in the end: which objective function can give better scores for correct topology given noise