PHASE : a software package for PHylogenetics And Sequence Evolution
This package is designed specifically for use with RNA sequences that have a conserved secondary structure, e.g., rRNA and tRNA. It is well known that compensatory substitutions occur in the paired regions of RNA secondary structures; this means that substitutions occurring on one side of a pair are correlated with substitutions on the other side. Most phylogenetic programs assume that each site in a molecule evolves independently of the others but this assumption is not valid for RNA genes.
PHylogenetics And Sequence Evolution的缩写，序列进化分析软件，使用手册，542K，PDF格式。