#NEXUS
BEGIN TAXA;
title some_family;
dimensions ntax=4;
taxlabels A B C D;
END;
BEGIN CHARACTERS;
title protein;
link taxa=some_family;
dimensions nchar=59;
format
datatype=protein
missing=?
gap=-
;
matrix
A -MQVADISLQG--DAKKGANLFKTRCAQCHTLKAGEGNKI-----------GPELHG-?
B -------MAGG--DIKKGANLFKTRCAQCHTVEKDGGNKI-----------GPALHG--
C -MG----FSAG--DLKKGEKLFTTRCAQCHTLKEGEGNKV-----------GPALHG--
D -MG--DVEKGKKIFVQKCAQCHTVEKGGKHKT------?----GPNLHG--LFGRKTGQ
;
END;
BEGIN TREES;
tree 'basic bush' = ((A:1,B:1):1,(C:1,D:1):1);
END;