How to generate the input for INSIGHT model

[datngu]

Dear Developers,

I am interested in the tool and would like to implement the score in another species. I have some questions in generating the INSIGHT model input.

While the input data for polymorphic sites are easy to obtain (typically can extract from a standard VCF file).
I have several questions:

• How can I divide the genome into blocks, what are the criteria? How can I estimate theta, lambda?
  block chr1:1100346-1105346 theta 0.00117596406302 lambda 0.00455034
• For monomorphic sites, how can I obtain "the prior probability that the deep ancestral state Zi equals the observed major allele (or the only observed allele in case of an 'M' site)" according to the description?
• How can I obtain the outgroup statistics? Can I start with Multiple Alignment from ensembl such as http://ftp.ensembl.org/pub/release-109/emf/ensembl-compara/multiple_alignments/10_primates.epo/

Looking for your help!
Best wishes,
Dat Nguyen