Tanglegram advice

[SeqTroubles]

Hello all,

Im looking to construct a tanglegram of core vs accessory genes. But I want to colour the associations by some metadata.

I have been using R package ape with cophyloplot but Ive not had any great success the colour of the lines in not accurate. I was wonder what do you use when you construct tanglegrams?

Thanks

[bsp017]

I used Dendroscope several years ago to compare fingerprints v gyrase B sequences. Not very customisable but maybe worth a try