recolour the alignment on the basis of percentage identity

[Yogesh Sharma]

hi 

i am trying to make a figure with phylotree and MSA. but i am facing some issues

1) phylogentic tree labels are not getting aligned to right. 

for example shown in this image 

http://wasabiapp.org/wp-content/uploads/2014/10/wasabi_upload.png

2) how do i recolour alignment according to percentage identity of residue at particular position. i want to make a colour scale from Iris Blue (low conservation)#0EB8C1, white and Lipstick#9B245D (high conservation)gradient

looking forward to your expert reviews and support