Here are examples of an alignment for input for the program "LCore".

If you have an alignment of protein structures, note that the names of sequences should be of the form:
PDBcode_Chain[_Model]

>1PER_L
SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTK-RPRFLPELASALGVS
VDWLLNGT
>1PER_R
SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTK-RPRFLPELASALGVS
VDWLLNGT
>1ADR_A_1
LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCS
PDYLLKGD
>1ADR_A_2
LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCS
PDYLLKGD

Here is an example of alignment of complexes. [(sequence):chain.type_of_atom/model]

&1NK2
(TGTGTCAAGTGGCTGT):A.P/1
(ACAGCCACTTGACACA):B.P/1
(ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEGHP):P.CA/1
&1NK2
(TGTGTCAAGTGGCTGT):A.P/2
(ACAGCCACTTGACACA):B.P/2
(ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEGHP):P.CA/2
&1NK2
(TGTGTCAAGTGGCTGT):A.P/3
(ACAGCCACTTGACACA):B.P/3
(ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEGHP):P.CA/3