To whom it may concern,

I am looking to calculate the Phastcons scores for the Human coding genes based on FASTA alignments of 27 vertebrate genomes with Human for CDS regions.

Firstly, in my case, how should I type the Phastcons COMMAND ON Unix. I saw the following examples on Phastcons HOWTO:

The program can be run with a command of the form:

phastCons [OPTIONS] alignment [cons.mod,]noncons.mod > scores.wig

For example,

phastCons --target-coverage 0.25 --expected-length 12 \
    --msa-format MAF alignment.maf cons.mod,noncons.mod \
    > scores.wig

or

phastCons --target-coverage 0.25 --expected-length 12 \
    --rho 0.4 --msa-format MAF alignment.maf noncons.mod \
    > scores.wig

I thought about:

phastCons "my alignment file" "??"  > scores.wig

?? = Instead of cons.mod,noncons.mod, what should I put? I thought about the .mod file that was used to calculate the PhastCons scores based on multiple alignments of 27 vertebrate genomes with Human. But the difference is that it was not only comparing the CDS regions, but the whole genome. Any ideas?

Looking forward to hearing from you soon,

Jeff O.