tree topology doesn't match with output from dendroscope ??

[limin321]

Hello,

I created three phylogenetic tree using three different methods, now I want to compare the topology of my three trees using phylogram r package, here is my codes and output:

# read dendrogram
dend1 <- read.dendrogram("tree1.newick")
dend2 <- read.dendrogram("tree2.newick")
dend3 <- read.dendrogram("tree3.newick")
# ladderizing
dend1 <- ladder(dend1, decreasing = TRUE)
dend2 <- ladder(dend2, decreasing = TRUE)
dend3 <- ladder(dend3, decreasing = TRUE)
# tanglegram two trees
dndlist <- dendextend::dendlist(dend1, dend2)
dendextend::tanglegram(dndlist, fast = FALSE, margin_inner = 5)

dndlist <- dendextend::dendlist(dend2, dend3)
dendextend::tanglegram(dndlist, fast = FALSE, margin_inner = 5)

The output of two tanglegram look like this:

However, I did same tanglegram analysis of above tree pairs in dendroscope, the outputs show the topology of my trees agree with each other, here is how they look like:

Can anyone have any recommendation on how to modify my codes so I can have the same output as from dendroscope??

Thank you so much.

Best,
LC