Quantify similarity between multi-fasta files

[robinweide]

Hi there,

I want to compare the output of de novo assemblies of multiple samples. From this, I'd like to cluster the samples on (dis)similarity.

With bla(s)t, I get per-sequences scores (which I could use to get a percentage of similar bases between the query and database). With CD-HIT (EST), I do get clusters, but still no score/percentage.

Does anybody have a more straightforward solution for this?

Seasons greetings,

Robin