## Posts

### Backward algorithm

### Forward algorithm

### Viterbi algorithm

### COMP571 (Fall 2020, a.k.a. COVID times)

### Calculating the likelihood for an ultrametric tree (example)

### Hill climbing and NNI

### Long branch attraction (in the Felsenstein zone)

### Likelihood of a tree

### Dollo's law and unequal-cost parsimony

### Equal-cost parsimony

### COMP571/BIOC571 (Fall 2019)

### Priors and clock models in StarBEAST2 tutorial

### Maximum Parsimony tutorial using PAUP

### Neighbor joining

### UPGMA and WPGMA trees

### GTR and nested models

### Tree comparisons

### Phylogenetic trees and data structures

### Hidden Markov models

### Markov models

### Pseudocounts

### Bayesian inference and MCMC

### Probability and likelihood distributions

### Position-specific score matrices

### Burrows–Wheeler transform

### Arrays and addressing

### Indexed MegaBLAST, BLAT, and SSAHA

### BLAST and FASTA

### PAM vs BLOSUM score matrices

### Expected values of score matrices

### Smith–Waterman

### Needleman–Wunsch

### Recursion

### COMP571/BIOC571

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