[Genome] Chained blastz alignments

[Eric Just]

Hello,

I have read some papers and some information on your site about generating
whole genome alignments.  I am using the technique of running BLASTZ and
then post-processing the data using axtChain then chainNet to generate the
non-overlapping gapped global alignements.  My question is about the C
argument to BLASTZ.  The BLASTZ output says:

        C(0) 0: no chaining; 1: just output chain; 2: chain and extend;  3:
just output HSPs

So can the use of the C argument obviate the need for chaining using
axtChain?  If not, what is the difference between chaining done by BLASTZ vs
chaining doen by chainNet?

Thanks for your time!

Eric