STAT 992 SJR CC

Statistics 992: Statistical Phylogenetics Professor: Oce: Phone: E-Mail: Web: Oce Hours: Class Hours: Room: Textbook: Bret Larget 4390 CSSC (Computer Science and Statistics Center) 262-7979 larget@stat.wisc.edu http:/www.stat.wisc.edu/~larget/ Wednes

Statistics 992 Homework #1: Due Friday, January 30 Spring 2004 Table 1: Dolphin Hippopotamus Camel Cow Giraffe Sperm whale Blue whale Pig Sheep Goat ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ACC ACA ACA ACT ATC ACC ACC ACC ATC ACC AAC AAC AAC AAC

Statistics 992 Solutions. Solutions to Homework #1 Spring 2004 1. Considering only the rst ve taxa, there are 21 unvaried sites which contribute nothing to the parsimony score of any tree. Sites 5, 12, 19, 28, and 30 have a single singleton and ad

Statistics 992 Homework #2: Due Friday, February 13 Spring 2004 Table 1: Dolphin Hippopotamus Camel Cow Giraffe ATG ATG ATG ATG ATG ACC ACA ACA ACT ATC AAC AAC AAC AAC AAC ATC ATC ATC ATT ATC CGA CGA CGA CGA CGA AAA AAA AAA AAG AAG ACA TCT

Statistics 992 Solutions: 1. The likelihood has the expression L(t) = Solutions to Homework #2 Spring 2004 1 4 n 1 3 4t + e3 44 n1 1 1 4t e3 44 n2 where n = n1 + n2 . We can simplify the analysis by using the transformation a = e 3 t and wo

Statistics 992 Continuous-time Markov Chains Spring 2004 Summary Continuous-time nite-state-space Markov chains are stochastic processes that are widely used to model the process of nucleotide substitution. This chapter aims to present much of the

Statistics 992 Homework #3: Due Friday, March 5 Spring 2004 If you have never used R or have no experience with computer programming, you may complete only problem 1 and 2 for full credit for the assignment. Others should complete all four problem

Statistics 992 1. The acceptance probability is Homework #3: Due Friday, March 5 Spring 2004 p( | = A acceptance prob. = min 1, p( | = A A 1 Q (A) i i i i (Ai ) = min 1, Q (A) ( i (i )Ai 1 ) i (Ai ) A 1 ( i (Ai ) i i i = min 1,

Statistical Science 2003, Vol. 18, No. 2, 241255 Institute of Mathematical Statistics, 2003 Bootstrapping Phylogenetic Trees: Theory and Methods Susan Holmes Abstract. This is a survey of the use of the bootstrap in the area of systematic and evolu