After running GARLI, I wanted to compare
OR137:
OR213: lots of disagreements; redo with 100
OR4: lots of disagreements; redo with 100
OR589: lot
OR6: all agree after 8 runs
OR10: all agree after 8 runs
OR11: tree2 disagrees, 7 others agree, use this as main gene tree
OR51: lots of disagreements; redo with 100
OR52: lots of disagreements; redo with 100

100 is a lot of tree to compare, so I wrote a small script doing so:

setwd("/Volumes/Yango/Hayden_batORs/garli/OR51/trees")

#tell where to open up all of your downloaded files from CIPRES
my.files<-list.files("/Volumes/Yango/Hayden_batORs/garli/OR51/trees/")
#read in all of these trees to a list using read.nexus function
my.trees<-lapply(my.files, read.nexus)

#create a matrix to store all of the tree comparisons
tree.matrix<-matrix(nrow = length(my.trees), ncol = length(my.trees))

for(i in 1:length(my.trees)){ #for every tree in the file
  this.tree<-as.phylo(my.trees[[i]]) #look at that tree
  #compare the topology to all the other trees
  tree.matrix[i,]<-sapply(my.trees, function(my.trees) dist.topo(this.tree,my.trees))
}
tree.matrix

#print out the ones that agree with each other
for(i in 1:length(tree.matrix[1,])){
  this.list<-as.numeric(which(tree.matrix[i,]==0))
  print(this.list)
}
write.csv(tree.matrix, "tree.matrix.csv")

For OR51, are things looking better?

[1] 1

[1] 2

[1] 3

[1]  4 84

[1] 5

[1] 6

[1] 7

[1]  8 15 41 79

[1]  9 14

[1] 10 54

[1] 11

[1] 12

[1] 13 73

[1]  9 14

[1]  8 15 41 79

[1] 16

[1] 17 20 75

[1] 18

[1] 19

[1] 17 20 75

[1] 21 51 68

[1] 22 37

[1] 23 50 71

[1] 24

[1] 25

[1] 26

[1] 27

[1] 28 69 88

[1] 29

[1] 30

[1] 31

[1] 32 46

[1] 33

[1] 34 70

[1] 35 53

[1] 36

[1] 22 37

[1] 38 59

[1] 39 47 78

[1] 40

[1]  8 15 41 79

[1] 42

[1] 43

[1] 44

[1] 45

[1] 32 46

[1] 39 47 78

[1] 48

[1] 49

[1] 23 50 71

[1] 21 51 68

[1] 52

[1] 35 53

[1] 10 54

[1] 55

[1] 56

[1] 57

[1] 58

[1] 38 59

[1] 60

[1] 61

[1] 62 86 87

[1] 63

[1] 64

[1] 65

[1] 66 95

[1] 67

[1] 21 51 68

[1] 28 69 88

[1] 34 70

[1] 23 50 71

[1] 72

[1] 13 73

[1] 74

[1] 17 20 75

[1] 76

[1] 77

[1] 39 47 78

[1]  8 15 41 79

[1] 80

[1] 81

[1] 82

[1] 83

[1]  4 84

[1] 85

[1] 62 86 87

[1] 62 86 87

[1] 28 69 88

[1] 89

[1] 90

[1] 91

[1] 92

[1] 93

[1] 94

[1] 66 95

[1] 96

[1] 97

[1] 98

Womp, womp...not really--only a maximum of 4 trees out of 100 are agreeing.

OR4s looking much better:
[1]  1 22 28 42 75
[1]  2 99
[1]  3 14 18 83 89
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1] 5
[1] 6
[1]  7 15 98
[1] 8
[1]  9 19 38 80
[1] 10 50
[1] 11 67
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1] 13 86
[1]  3 14 18 83 89
[1]  7 15 98
[1] 16
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1]  3 14 18 83 89
[1]  9 19 38 80
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1] 21 31 44 62 84
[1]  1 22 28 42 75
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1] 25
[1] 26
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1]  1 22 28 42 75
[1] 29
[1] 30 33
[1] 21 31 44 62 84
[1] 32 37 61 68 81
[1] 30 33
[1]  34 100
[1] 35
[1] 36
[1] 32 37 61 68 81
[1]  9 19 38 80
[1] 39 71
[1] 40 49
[1] 41
[1]  1 22 28 42 75
[1] 43
[1] 21 31 44 62 84
[1] 45
[1] 46
[1] 47
[1] 48
[1] 40 49
[1] 10 50
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1] 52
[1] 53
[1] 54
[1] 55
[1] 56 90
[1] 57
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1] 60
[1] 32 37 61 68 81
[1] 21 31 44 62 84
[1] 63
[1] 64
[1] 65
[1] 66
[1] 11 67
[1] 32 37 61 68 81
[1] 69
[1] 70
[1] 39 71
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1] 73
[1] 74
[1]  1 22 28 42 75
[1] 76
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1] 78
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1]  9 19 38 80
[1] 32 37 61 68 81
[1] 82
[1]  3 14 18 83 89
[1] 21 31 44 62 84
[1] 85
[1] 13 86
[1] 87
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1]  3 14 18 83 89
[1] 56 90
[1] 91
[1] 92
[1] 93
[1] 94
[1] 95
 [1]  4 12 17 20 23 24 27 51 58 59 72 77 79 88 96
[1] 97
[1]  7 15 98
[1]  2 99
[1]  34 100