Common substitution matrices for alignments.
When in doubt, use BLOSUM62. Consult http://www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml#20051206 for some hints on good parameters for nucleotide alignments.
See also http://en.wikipedia.org/wiki/Substitution_matrix for a summary about the difference between the different matrices.
For BLOSUM matrices, the associated number determines the similarity of the sequences the matrices are derived from.
Henikoff, S. and Henikoff, J. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA. 89(biochemistry): 10915 - 10919 (1992).
For PAM matrics, the number indicates the number of mutations that have occurred between the sequences that are compared.
Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. A model of evolutionary change in proteins. In "Atlas of Protein Sequence and Structure" 5(3) M.O. Dayhoff (ed.), 345 - 352 (1978).
BLASTn defaults, for nucleotide sequences
Blast defaults, use with gap_open = -5 gap_extend = -3 This should really check for valid nucleotides, and perhaps be more lenient in the case of Ns. Oh well.