The brief usage of options is as follows. The [ ] denote optional parts of the syntax:
options
-a[ll] select All sequences
-degap[=-] remove gap symbols
-i[tem=2,3,4] select Item number(s) from several
-l[ist] List sequences only
-r[everse] change to Reverse-complement
Pretty format options:
-wid[th]=# sequence line width
-tab=# left indent
-col[space]=# column space within sequence line on output
-gap[count] count gap chars in sequence numbers
-nameleft, -nameright[=#] name on left/right side [=max width]
-nametop name at top/bottom
-numleft, -numright seq index on left/right side
-numtop, -numbot index on top/bottom
-match[=.] use match base for 2..n species
-inter[line=#] blank line(s) between sequence blocks