I have multiple sequence alignments (MSAs) of clusters of sequences. I would like to know how I assess whether my MSA is informative enough (or say diverse enough) to apply sequence analysis tools like finding conserved positions or specificity determining positions. When I use Scorecons (http://www.ebi.ac.uk/thornton-srv/databases/valdarprograms/scorecons_server_help.html), it gives me a Dops score (diversity of alignment score) which helps me to an extent (100 for very informative or diverse sequences in a cluster and 0 for all exactly similar sequences in a MSA). However, I do not know the lowest/threshold Dops score which can be used. Also if there are any other ways of finding the same, kindly let me know how everyone tackles this problem.
I guess otherwise the results of the sequence analysis would not make sense at all, right?