The NEXUS format is used by software such as MrBayes and PAUP. It is not just a simple multiple alignment format, it can also contain a wealth of meta data regarding the alignment as well as commands for a program reading the NEXUS file to execute.
The NEXUS file format is comprised a “blocks” such as the taxa block, data block, sets block, trees block, PAUP block and MrBayes block, to name a few. Each block starts with begin <block name>; and ends with end;.
Software reading the NEXUS format should be able to process the file and skip any blocks that it does not understand. In writing a NEXUS file, data should be written to a “block” which is most appropriate and follows the convention set down by Madison before writing the data to a new type of block. For example, MrBayes currently requires TAXSETs to be defined in the MrBayes block. However, the appropriate place for these definitions in the SETS block so they are available to other NEXUS file readers.
Software commands can be included in a block which is to be read only by the intended software. This is usually done so as to allow batch processing of files by executing many commands in succession without the need to sit at the computer and enter them manually. For example the PAUP block and MrBayes block contain commands pertinent to their respective software.
Two main parts of the NEXUS file, which are describe in more detail below, are the Alignment and the Tree sections.
#NEXUS
[TITLE: NoName]
begin data;
dimensions ntax=3 nchar=384;
format interleave datatype=protein gap=- symbols="FSTNKEYVQMCLAWPHDRIG";
matrix
CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ----
ALEU_HORVU MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG
CATH_HUMAN ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK----
CYS1_DICDI --------SQ FLEFQDKFNK KY-SHEEYLE RFEIFKSNLG KIEELNLIAI
ALEU_HORVU ALGRTRHALR FARFAVRYGK SYESAAEVRR RFRIFSESLE EVRSTN----
CATH_HUMAN --------FH FKSWMSKHRK TY-STEEYHH RLQTFASNWR KINAHN----
CYS1_DICDI NHKADTKFGV NKFADLSSDE FKNYYLNNKE AIFTDDLPVA DYLDDEFINS
ALEU_HORVU RKGLPYRLGI NRFSDMSWEE FQATRL-GAA QTCSATLAGN HLMRDA--AA
CATH_HUMAN NGNHTFKMAL NQFSDMSFAE IKHKYLWSEP QNCSAT--KS NYLRGT--GP
CYS1_DICDI IPTAFDWRTR G-AVTPVKNQ GQCGSCWSFS TTGNVEGQHF ISQNKLVSLS
ALEU_HORVU LPETKDWRED G-IVSPVKNQ AHCGSCWTFS TTGALEAAYT QATGKNISLS
CATH_HUMAN YPPSVDWRKK GNFVSPVKNQ GACGSCWTFS TTGALESAIA IATGKMLSLA
CYS1_DICDI EQNLVDCDHE CMEYEGEEAC DEGCNGGLQP NAYNYIIKNG GIQTESSYPY
ALEU_HORVU EQQLVDCAGG FNNF------ --GCNGGLPS QAFEYIKYNG GIDTEESYPY
CATH_HUMAN EQQLVDCAQD FNNY------ --GCQGGLPS QAFEYILYNK GIMGEDTYPY
CYS1_DICDI TAETGTQCNF NSANIGAKIS NFTMIP-KNE TVMAGYIVST GPLAIAADAV
ALEU_HORVU KGVNGV-CHY KAENAAVQVL DSVNITLNAE DELKNAVGLV RPVSVAFQVI
CATH_HUMAN QGKDGY-CKF QPGKAIGFVK DVANITIYDE EAMVEAVALY NPVSFAFEVT
CYS1_DICDI E-WQFYIGGV F-DIPCN--P NSLDHGILIV GYSAKNTIFR KNMPYWIVKN
ALEU_HORVU DGFRQYKSGV YTSDHCGTTP DDVNHAVLAV GYGVENGV-- ---PYWLIKN
CATH_HUMAN QDFMMYRTGI YSSTSCHKTP DKVNHAVLAV GYGEKNGI-- ---PYWIVKN
CYS1_DICDI SWGADWGEQG YIYLRRGKNT CGVSNFVSTS II--
ALEU_HORVU SWGADWGDNG YFKMEMGKNM CAIATCASYP VVAA
CATH_HUMAN SWGPQWGMNG YFLIERGKNM CGLAACASYP IPLV
BEGIN TREES;
TRANSLATE
1 Struthio_camelus,
2 Rhea_americana,
3 Pterocnemia_pennata,
4 Casuarius_casuarius,
5 Dromaius_novaehollandiae,
6 Nothoprocta_cinerascens,
7 Eudromia_elegans,
8 Pygoscelis_adeliae_f,
9 Pygoscelis_adeliae_y,
10 Spheniscus_humboldti,
11 Phalacrocorax_sulcirostris,
12 Anhinga_novaehollandeae,
13 Nycticorax_nycticorax,
14 Chauna_chavaria,
15 Anseranas_semipalmata,
16 Dendrocygna_arcuata,
17 Dendrocygna_autumnalis,
18 Dendrocygna_eytoni_d,
19 Dendrocygna_eytoni_e,
20 Dendrocygna_viduata,
21 Coscoroba_coscoroba,
22 Cygnus_atratus,
23 Goose,
24 Anser_indicus,
25 Branta_canadensis,
26 Cereopsis_novaehollandiae,
27 Chloephaga_picta,
28 Duck,
29 Anas_platyrhynchos,
30 Megapodius_freycinet,
31 Leipoa_ocellata,
32 Ortalis_vetula,
33 Penelope_jacquacu,
34 Penelope_superciliaris,
35 Bonasa_umbellus,
36 Tympanuchus_cupido,
37 Oreortyx_pictus,
38 Callipepla_squamata_n,
39 Callipepla_squamata_s,
40 Lophortyx_californicus,
41 Colinus_virginianus,
42 Cyrtonyx_montezumae_l,
43 Cyrtonyx_montezumae_s,
44 Alectoris_chukar,
45 Alectoris_rufa,
46 Francolinus_afer,
47 Francolinus_erckelii,
48 Francolinus_coqui_v,
49 Francolinus_coqui_a,
50 Francolinus_francolinus_a,
51 Francolinus_francolinus_v,
52 Francolinus_pondicerianus,
53 Perdix_perdix,
54 Coturnix_delegorguei,
55 Coturnix_coturnix_japonica_1,
56 Coturnix_coturnix_japonica_2,
57 Arborophilia_torqueola,
58 Bambusicola_thoracica,
59 Tragopan_satyra,
60 Tragopan_temmincki,
61 Lophophorus_impejanus,
62 Crossoptilon_auritum,
63 Lophura_edwardsi,
64 Lophura_ignita,
65 Gallus_gallus,
66 Grey_jungle_fowl,
67 Phasianus_colchicus,
68 Syrmaticus_ellioti,
69 Syrmaticus_reevesii,
70 Chrysolophus_amherstiae,
71 Polyplectron_bicalcaratum,
72 Argusianus_argus_argus,
73 Pavo_cristatus,
74 Afropavo_congensis,
75 Numida_meleagris,
76 Acryllium_vulturinum,
77 Meleagris_gallopavo,
78 Grus_carunculatus,
79 Anthropoides_virgo,
80 Grus_vipio,
81 Fulica_atra,
82 Vanellus_spinosus,
83 Larus_rudibundus,
84 Turnix_sylvatica,
85 Gallirallus_australis,
86 Geococcyx_californianus,
87 Dacelo_novaeguineae,
88 Carpococcyx_renauldi,
89 Podargus_strigoides
;
TREE * PAUP_1 = [&R] (1,(((2,3),(4,5)),((((((((((6,7),((30,31),(((32,33),34),(((((((35,57),((((53,67),70),(62,(63,64),(68,69))),
(((54,(55,56)),84),74))),(((46,(48,49)),47),71)),((36,59),60),(61,(75,76))),(72,73),77),((44,45),((((50,51),58),52),(65,66)))),
(((37,((38,39),40)),41),(42,43)))))),14),15),((((16,20),(18,19)),17),((((21,26),(27,(28,29))),22),((23,24),25)))),(78,79,80)),87),
((81,85),(82,83))),(8,9,(10,((11,(86,88)),13),12))),89)));
END;
http://www.ncbi.nlm.nih.gov/pubmed/11975335