# netdir/species1/species2/net/chr?.net
>netdir
/home/jianma/net

# chaindir/species1/species2/chain/chr?.chain
>chaindir
/home/jianma/net

# species-name tag (0: ref-species, 1: descendents, 2: outgroup)
>species
hg18 0
rheMac2 1
mm9     1
rn4     1
bosTau3 1
canFam2 1
galGal3 2
monDom4 2

# phylogenetic tree with branch lengths. @ symbol indicates the target ancestor.
>tree
(((((hg18:0.03685897,rheMac2:0.03685897):0.06169872,(mm9:0.01602564,rn4:0.01602564):0.08253205):0.05416667,(bosTau3:0.15272436,canFam2:0.15272436):0.08413462)@:0.04695513,monDom4:0.1996795):0.3003205,galGal3:0.5)