"topologyprofile"<-function(basename){
seqlength<-scan(paste(basename,".phy",sep=""),nlines=1,quiet= TRUE)[2]
tps <- rJava::.jnew("TopologyProfile", paste(basename,".post",sep=""),paste(basename,".topoprob",sep=""),paste(basename,".tree",sep=""),as.integer(seqlength))
#system(paste("java TopologyProfile ",basename,".post ",basename,".topoprob ",basename,".tree ",seqlength,sep=""))
}
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