`aligned fasta` format is not the same as `plain fasta` format. Just making sure. example of an aligned fasta file below

>APE_PIG
MRVLWVALVVTLLAGCRTEDEPGPPPE.VHVWWEESKWQGSQP.WEQALGRFWDYLRWVQ
SLSDQVQEELLSTKVTQELTELIEESMKEVKAYREELEAQLGPVTQETQARLSKELQAAQ
ARVGADMEDVRNRLVLYRSEVHNMLGQTTEELRSRLASHLRNVRKRLVRDTEDLQKRLAV
YQAGLREGAERSVSALRERLGPLVEQGRLRAATLSTRAGQPLRERAEAWGQKLRGRLEEM
GSRTRDRLDEMRDELEEVRTKVEEQGSQLRLQAEAFQARLKGWFEPLVEDMRRQWAGLVE
RMQSAVSISSSTSA..PSDNQ
>APE_MOUSE
MKALWAVLLVTLLTGCLA........EGEPEVTDQLEWQSNQP.WEQALNRFWDYLRWVQ
TLSDQVQEELQSSQVTQELTALMEDTMTEVKAYKKELEEQLGPVAEETRARLGKEVQAAQ
ARLGADMEDLRNRLGQYRNEVHTMLGQSTEEIRARLSTHLRKMRKRLMRDAEDLQKRLAV
YKAGAREGAERGVSAIRERLGPLVEQGRQRTANLGAGAAQPLRDRAQAFGDRIRGRLEEV
GNQARDRLEEVREHMEEVRSKMEEQTQQIRLQAEIFQARLKGWFEPIVEDMHRQWANLME
KIQASVATNPII.TPVAQENQ



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