Hey all,

This is my first time to calculate conservation scores and i have a problem.

I have 106 interval in hg19. I want to have the conservation scores for these parts for different species. To do that, i prepared maf file with my 106 region interval file using uscs multi100way.

I also downoaded multi100way tree Newick format from UCSC.

However, when i run the phastcons:

 phast % phastCons --msa-format MAF mypath/maffile3.maf /mypath/hg19.100way.commonNames.nh > scores.txt

i got the following error:

Reading tree model from /Users/xxxxx/Downloads/hg19.100way.nh...

ERROR: unrecognized tag in model file ("((((((((((((((((((hg19:0.00641635,").

i couldn't understand the problem, i checked the newick file and my maf file and everything looks fine.

i will be happy to see the recommended solutions

thanks