phylogenetics

construct a data matrix

identify a tree that i most compatible with the data matrix

conduct statistical analyses to evaluate confidence

ingroup

outgroup

serves as a point of comparison

for rooting of a phylogeny to determine the polarity of character change

gap penalty

penalize alignments that add indels

threshold for the no of base substitutions avoided 

before an indel is inferred (often 3-20)

evolutionary model

base freq

substitution rate matrix

gamma distribution (among-site rate variation)

proportion of invariable sites

Jukes-Cantor model, JC, JC69

F81, Felsenstein 1981, higher GC, more stable

HYK85, HYK, Hasgawa Kishino Yano 1985, higher rate transitions than transversions

GTR, General Time Reversible

GTR + I + r, proportion of invariable sites, rate heterogeneity, conserved DNA parts

AIC, Akaike's Information Criterion, information theory

LRT, Likelihood Ration Test, frequentist hypothesis testing

DT, Decision Theoretic Risk, decision theory

BF, Bayes Factors, bayesian model testing

PP, Posterior probabilities, bayesian hypothesis testing

BIC, Bayesian Informarion Criterion, mix of bayesian motivation and information theory

hLRT, Hierarchical likelihood ratio test

Maximum Parsimony (minimize the amount of homoplasy, fewest character state changes 단순인색절약성, brach and bound, heuristic search, not for mole data)

Neighbor Joining (distance, average number of substitutions/site, for a quick approximation)

Maximum Likelihood (highest probability of data given the tree)

Bayesian Inference (...subjective degree of belief, Markoc Chain, memoryless, Monte Carlo, repeated random sampling, accept the new point if it is higher posterior probability)

and Bootstrap