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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 […] http://www.r-phylo.org/wiki/HowTo/InputtingTrees 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: library(ape) This loads the package ape and its required packages, gee, nlme and lattice, into your R […] |
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