# 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
hg     2
mm     2
rn     2
cattle 1
canFam 1
cat    0
pig    1

# phylogenetic tree with branch lengths. @ symbol indicates the target ancestor.
>tree
((hg:0,09855769,(mm:0.01602564,rn:0.01602564):0.08253205):0.05416667,((cattle:0.07740385,pig:0.07740385):0.07532051,(canFam:0.06858974,cat:0.06858974):0.08413462)@:0.0)