How to compare the alignment quality of two or more homology modelling software

Question

[roonymoonlight]

Hi

I am generating a high quality model by homology modeling method. But I am looking at alignment from different software , alignment between my target sequences from blast and other alignmet from HHpred. saw I want to compare the quality of the two alignment , any suggestion how can I do that ?

[microfuge]

t-coffee provides good alignment comparison methods for structural alignments here