> ## this script takes semistrict data and outputs the maximal parsimony (MP) tree
> ## it also uses bootstrapped trees to produce majority rule consensus
> 
> library(phangorn) # will be used to estimate MP tree, no external tool needed
Loading required package: ape

> library(shipunov)
package 'shipunov', version 1.5-1

> DATE <- format(Sys.time(), "%Y%m%d_%H%M%S") # timestamp

> treesp <- read.table("_kubricks_treesp.txt", sep="\t", h=TRUE, as.is=TRUE) # read treesp to understand outgroups and outlliers

> outgroups <- treesp$SPECIES.NEW[treesp$TYPE == "outgroup" & treesp$USE == 1]

> outgroups <- gsub(" ", "_", outgroups)

> conc <- read.dna("40_concatenated/semistrict.fasta", format="fasta")

> LAB <- sub("__.*$", "", labels(conc))

> OUT <- labels(conc)[LAB %in% outgroups]

> outliers <- treesp$SPECIES.NEW[treesp$TYPE == "outlier" & treesp$USE == 1]

> if (length(outliers) > 0) {
+  outliers <- gsub(" ", "_", outliers)
+  EXC <- labels(conc)[LAB %in% outliers]
+  conc <- conc[!labels(conc) %in% EXC, ] # remove outliers, if any
+ }

> conc.phydat <- phyDat(conc) # "phangorn" requires everything in its own format

> tr1 <- NJ(dist.hamming(conc.phydat)) # make starting tree

> conc.pr <- pratchet(conc.phydat, maxit=100, k=20, start=tr1) # change these parsimony ratchet parameters if needed
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"

> if (!is.binary(conc.pr)) conc.pr <- multi2di(conc.pr) # sometimes, trees are not binary

> conc.pr <- acctran(conc.pr, conc.phydat)

> conc.ptrees <- bootstrap.phyDat(conc.phydat, pratchet, bs=100, multicore=TRUE) # change bootstrap replications if needed
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 117"[1] "Best pscore so far: 107"

[1] "Best pscore so far: 115"
[1] "Best pscore so far: 107"
[1][1] "Best pscore so far: 117"
 "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 107"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 121"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 107"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 108"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 108"
[1] "Best pscore so far: 136"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 136"
[1] "Best pscore so far: 108"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 136"
[1] "Best pscore so far: 108"
[1] "Best pscore so far: 126"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 136"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 108"[1] "Best pscore so far: 126"

Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 136"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 108"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 136"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 136"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 108"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 136"
[1] "Best pscore so far: 108"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 136"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 108"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 136"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 108"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 136"
[1] "Best pscore so far: 108"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 125"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 125"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 138"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 125"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 138"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 125"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 138"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 125"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 138"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 125"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 138"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 125"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 138"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 125"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 125"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 138"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 125"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 138"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 125"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 138"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 123"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 138"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 123"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 138"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 139"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 139"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 139"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 139"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 139"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 139"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 139"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 139"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 139"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 139"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 139"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 133"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 94"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 94"
[1] "Best pscore so far: 115"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 94"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 132"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 94"
[1] "Best pscore so far: 115"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 94"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 94"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 94"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 113"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 94"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 94"
[1] "Best pscore so far: 113"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 94"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 113"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 94"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 113"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 113"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 124"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 124"
[1][1] "Best pscore so far: 112"
 "Best pscore so far: 111"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 111"
[1][1] "Best pscore so far: 112"
 "Best pscore so far: 124"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 106"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 106"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 106"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 106"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 106"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 106"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 106"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 106"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 126"
[1][1] "Best pscore so far: 107" "Best pscore so far: 106"

[1] "Best pscore so far: 123"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 106"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 106"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 107"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 114"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 114"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 114"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 114"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 114"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 114"
[1] "Best pscore so far: 114"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 114"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 105"
[1] "Best pscore so far: 114"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 105"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 114"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 114"
[1] "Best pscore so far: 105"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 105"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 105"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 105"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 105"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 105"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 105"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 105"
[1] "Best pscore so far: 122"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 105"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 102"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 102"
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 102"
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 102"
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 102"
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 102"
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 102"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 102"
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 126"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 102"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 110"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 130"
[1][1] "Best pscore so far: 110"
 "Best pscore so far: 119"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 130"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 126"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 129"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 99"
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 129"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 99"
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 129"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 99"
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 129"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 99"
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 129"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 99"
[1] "Best pscore so far: 129"
[1] "Best pscore so far: 121"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 129"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :[1] "Best pscore so far: 121"

  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 99"
[1] "Best pscore so far: 129"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 121"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 99"
[1] "Best pscore so far: 129"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 121"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 125"
[1] "Best pscore so far: 99"
[1] "Best pscore so far: 129"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 125"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 99"
[1] "Best pscore so far: 125"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 125"
[1] "Best pscore so far: 99"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 125"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 99"
[1] "Best pscore so far: 125"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 125"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 125"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 125"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 125"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 125"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 128"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 128"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 128"
[1] "Best pscore so far: 100"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 128"
[1] "Best pscore so far: 100"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 100"
[1] "Best pscore so far: 128"
[1][1] "Best pscore so far: 128"
 "Best pscore so far: 100"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 100"
[1] "Best pscore so far: 128"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 100"
[1] "Best pscore so far: 128"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 100"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 128"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 100"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 128"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 100"
[1] "Best pscore so far: 128"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 100"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 122"Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :

  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 100"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 109"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 103"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 109"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 103"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 103"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :[1] "Best pscore so far: 109"

  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 103"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 109"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 103"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 109"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 103"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :[1] "Best pscore so far: 122"

  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 109"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1][1] "Best pscore so far: 111"
 "Best pscore so far: 122"
[1] "Best pscore so far: 103"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 109"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 103"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 122"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 109"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 103"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 109"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 103"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 112"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 103"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 112"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 134"
[1] "Best pscore so far: 112"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 134"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 112"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 112"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 122"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 132"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 92"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 132"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 92"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 92"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 92"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 92"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 92"
[1] "Best pscore so far: 132"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 97"
[1] "Best pscore so far: 92"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 97"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 97"
[1] "Best pscore so far: 92"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 97"
[1] "Best pscore so far: 115"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 92"
[1] "Best pscore so far: 97"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 92"
[1] "Best pscore so far: 97"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 97"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 92"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 97"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 116"
[1] "Best pscore so far: 97"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 116"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 97"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 97"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 116"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 98"
[1] "Best pscore so far: 101"
[1] "Best pscore so far: 116"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :[1] "Best pscore so far: 98"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all

  some trees were rooted, unrooted all
[1] "Best pscore so far: 119"
[1] "Best pscore so far: 101"
[1] "Best pscore so far: 98"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 116"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 101"
[1] "Best pscore so far: 98"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 116"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 101"
[1] "Best pscore so far: 98"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 120"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 116"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 101"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 98"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 116"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 101"
[1] "Best pscore so far: 98"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 116"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 98"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 101"
[1] "Best pscore so far: 120"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 116"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 98"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 101"
[1] "Best pscore so far: 120"
[1] "Best pscore so far: 116"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 98"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 120"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 101"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 98"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 109"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 101"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 101"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 110"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 111"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 130"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 130"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 124"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1][1] "Best pscore so far: 118"
 "Best pscore so far: 109"
[1] "Best pscore so far: 130"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 130"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 109"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 130"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 128"
[1] "Best pscore so far: 130"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 128"
[1] "Best pscore so far: 124"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 130"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 130"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 130"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 130"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 104"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 130"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 104"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 104"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 104"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 104"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 104"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 104"
[1] "Best pscore so far: 123"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 118"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 127"
[1] "Best pscore so far: 104"
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
Warning in mRF2(tree1, tree2, normalize, check.labels, rooted) :
  some trees were rooted, unrooted all
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 118"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 98"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 98"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 123"
[1] "Best pscore so far: 98"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 98"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 98"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 98"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 110"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 98"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 98"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 111"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 135"
[1] "Best pscore so far: 98"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 135"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 98"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 135"
[1] "Best pscore so far: 113"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 135"
[1] "Best pscore so far: 98"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 135"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 117"
[1] "Best pscore so far: 135"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 135"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 135"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 135"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 135"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 135"
[1] "Best pscore so far: 133"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 133"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 133"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 133"
[1] "Best pscore so far: 115"
[1] "Best pscore so far: 133"
[1] "Best pscore so far: 133"
[1] "Best pscore so far: 133"
[1] "Best pscore so far: 133"
[1] "Best pscore so far: 133"
[1] "Best pscore so far: 133"
[1] "Best pscore so far: 133"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 122"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 121"
[1] "Best pscore so far: 121"

> conc.prr <- Root1(conc.pr, OUT, resolve.root=TRUE) # Root1() does not fail if unable to root on > 1 outgroup

> ## write tree to PDF
> pdf(paste0("99_trees/", DATE, "_semistrict_mp_kubricks.pdf"), height=8, width=12)

> oldpar <- par(mar=rep(0, 4))

> conc.prr.b <- plotBS(conc.prr, conc.ptrees, p=50, type="phylogram")

> add.scale.bar()

> mtext("semistrict MP", font=2, line=-1)

> par(oldpar)

> dev.off()
null device 
          1 

> ## keep tree as Newick file
> conc.prr.b$node.label[conc.prr.b$node.label == "NA"] <- "" # useful for some Newick reading software

> write.tree(conc.prr.b, file=paste0("99_trees/", DATE, "_semistrict_mp_kubricks.tre"))

> ## also save all bootstrapped treea as R object for later use
> dput(conc.ptrees, file=paste0("99_trees/", DATE, "_strict_mp_ptrees_kubricks.rd"))

> ## calculate majority rule consensus
> cons.50 <- consensus(conc.ptrees, p=0.5) # change if you need other consensus criteria

> cons.50r <- Root1(cons.50, OUT)

> ## write consensus tree to PDF
> pdf(paste0("99_trees/", DATE, "_semistrict_mp_consensus_kubricks.pdf"), height=8, width=12) # change PDF size if needed

> oldpar <- par(mar=rep(0, 4))

> conc.prr.b <- plot(cons.50r)

> add.scale.bar()

> mtext("semistrict MP, majority rule consensus", font=2, line=-1)

> par(oldpar)

> dev.off()
null device 
          1