MrBayes Tree

Use clustalw to generate nexus format file

#NEXUS BEGIN DATA; dimensions ntax=55 nchar=534; format missing=? symbols=”ABCDEFGHIKLMNPQRSTUVWXYZ” interleave datatype=DNA gap= -;

Change to as follows: #NEXUS BEGIN DATA; dimensions ntax=55 nchar=534; format datatype=dna interleave=yes gap=- missing=?;

then type mb -i *.nex

MrBayes > lset nst=6 rates=invgamma

Setting Nst to 6 Setting Rates to Invgamma Successfully […]

HowTo/InputtingTrees (R language)

The commands referenced below are all part of special phylogenetic packages in R, not the basic R install. Be sure that you have installed and loaded the packages containing the commands referenced below before continuing. For example:


This loads the package ape and its required packages, gee, nlme and lattice, into your R […]