/usr/share/EMBOSS/test/data/protalign.nxs is in emboss-test 6.6.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | #NEXUS
BEGIN DATA;
dimensions ntax=5 nchar=272;
format missing=?
symbols="ABCDEFGHIKLMNOPQRSTUVWXYZ"
interleave datatype=PROTEIN gap= -;
matrix
uniprot|P48347|14310_ARATH ------MENEREKQVYLAKLSEQTERYDEMVEAMKKVAQLDV---ELTVE
uniprot|Q9S9Z8|14311_ARATH ------MENERAKQVYLAKLNEQAERYDEMVEAMKKVAALDV---ELTIE
uniprot|Q9C5W6|14312_ARATH -MSSSGSDKERETFVYMAKLSEQAERYDEMVETMKKVARVNS---ELTVE
uniprot|P93207|14310_LYCES MAALIPENLSREQCLYLAKLAEQAERYEEMVQFMDKLVLNSTPAGELTVE
uniprot|P42643|14331_ARATH -MATPGASSARDEFVYMAKLAEQAERYEEMVEFMEK-VAKAVDKDELTVE
uniprot|P48347|14310_ARATH ERNLVSVGYKNVIGARRASWRILSSIEQKEESKGNDENVKRLKNYRKRVE
uniprot|Q9S9Z8|14311_ARATH ERNLLSVGYKNVIGARRASWRILSSIEQKEESKGNEQNAKRIKDYRTKVE
uniprot|Q9C5W6|14312_ARATH ERNLLSVGYKNVIGARRASWRIMSSIEQKEESKGNESNVKQIKGYRQKVE
uniprot|P93207|14310_LYCES ERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRKNEEHVHLVKEYRGKVE
uniprot|P42643|14331_ARATH ERNLLSVAYKNVIGARRASWRIISSIEQKEESRGNDDHVSLIRDYRSKIE
uniprot|P48347|14310_ARATH DELAKVCNDILSVIDKHLIPSSNAVESTVFFYKMKGDYYRYLAEFSSGAE
uniprot|Q9S9Z8|14311_ARATH EELSKICYDILAVIDKHLVPFATSGESTVFYYKMKGDYFRYLAEFKSGAD
uniprot|Q9C5W6|14312_ARATH DELANICQDILTIIDQHLIPHATSGEATVFYYKMKGDYYRYLAEFKTEQE
uniprot|P93207|14310_LYCES NELSQVCAGILKLLESNLVPSATTSESKVFYLKMKGDYYRYLAEFKIGDE
uniprot|P42643|14331_ARATH TELSDICDGILKLLDTILVPAAASGDSKVFYLKMKGDYHRYLAEFKSGQE
uniprot|P48347|14310_ARATH RKEAADQSLEAYKAAVAAAENGLAPTHPVRLGLALNFSVFYYEILNSPES
uniprot|Q9S9Z8|14311_ARATH REEAADLSLKAYEAATSSASTELSTTHPIRLGLALNFSVFYYEILNSPER
uniprot|Q9C5W6|14312_ARATH RKEAAEQSLKGYEAATQAASTELPSTHPIRLGLALNFSVFYYEIMNSPER
uniprot|P93207|14310_LYCES RKQAAEDTMNSYKAAQEIALTDLPPTHPIRLGLALNFSVFYFEILNSSDK
uniprot|P42643|14331_ARATH RKDAAEHTLTAYKAAQDIANSELAPTHPIRLGLALNFSVFYYEILNSPDR
uniprot|P48347|14310_ARATH ACQLAKQAFDDAIAELDSLNEESYKDSTLIMQLLRDNLTLWTSDLNEEGD
uniprot|Q9S9Z8|14311_ARATH ACHLAKRAFDEAIAELDSLNEDSYKDSTLIMQLLRDNLTLWTSDLEEGGK
uniprot|Q9C5W6|14312_ARATH ACHLAKQAFDEAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDLPEDGG
uniprot|P93207|14310_LYCES ACSMAKQAFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDAQDQLD
uniprot|P42643|14331_ARATH ACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWASDMQDDVA
uniprot|P48347|14310_ARATH ERTKGADEPQDEN---------
uniprot|Q9S9Z8|14311_ARATH ----------------------
uniprot|Q9C5W6|14312_ARATH EDNIKTEESKQEQAKPADATEN
uniprot|P93207|14310_LYCES ES--------------------
uniprot|P42643|14331_ARATH DDIKEAAPAAAKPADEQQS---
;
end;
|