Update multiple_sequence_alignment.md

TeachingMaterials/multiple_sequence_alignment.md

@@ -19,6 +19,16 @@ Availability: Clustal Omega can be used via the web interface available at http:
 
 Input: It requires protein accession IDs or protein seqences in FASTA format. 
 
+[Frequently asked questions](http://www.ebi.ac.uk/Tools/msa/clustalo/help/faq.html#1)
+
+````
+What substitution matrix/default parameters are used by Clustal Omega?
+
+Clustal Omega uses the HHalign algorithm and its default settings as its core alignment engine. The algorithm is described in Söding, J. (2005) 'Protein homology detection by HMM–HMM comparison'. Bioinformatics 21, 951-960.
+
+The default transition matrix is Gonnet, gap opening penalty is 6 bits, gap extension is 1 bit.
+````
+
 ### Examples:
 
 To extract examples, we will review our first session of NCBI using following instructions: