annotate test-data/avian_ovomucoids.nex @ 0:25da76152cf2 draft

planemo upload commit 9d6eccd6006feba67862137cb9a1d743798f71d3-dirty

#NEXUS 

[ Data from: Laskowski, M., Jr., and W.M. Fitch.  1989.  Evolution of avian ovomucoids and of birds.
             Pp. 371-387 in B. Fernholm, K. Bremer, and H. Jornvall (eds.), The Hierarchy of Life. Elsevier Press, Amsterdam. ]

begin data;
	dimensions ntax=89 nchar=88;
	format datatype=protein missing=? gap=- matchchar=.;

	matrix
	[                                        10        20        30        40        50        60        70        80       ]
	[                                        .         .         .         .         .         .         .         .        ]
	Struthio_camelus                VKYPNTNEEGKEVVLPKILSPIGSDGVYSNELANIEYTNVSK??????FAT--VDDYKPVPLDYMLDSKTSNKNNVVESSGTLRHFGK
	Rhea_americana                  .............L..E..N.V.T................?.D?????...--...H...S.E..........D.....N...S....
	Pterocnemia_pennata             .............L..E..N.V.A..................DHD?EV...--...H...S.E..........D.....N...S....
	Casuarius_casuarius             ........D....L.....N.........DD......A....DHDKEV...--..E....SPE.......N..DS....N...G....
	Dromaius_novaehollandiae        ........D....L.....N..........D......A..??D?????...--.......S.E.......N..D.....N...G....
	Nothoprocta_cinerascens         .....A.D.....P...TP...A.NA.FGS....V....I..DHDK?????T-..G...AT.E.F..NQ.A..A....KNV....L..
	Eudromia_elegans                .R.....D.....P...TP..V.AN....S....V....I?.?????????S-I.G...AT.EFF..NQ....A.A..KNV..N.I.E
	Pygoscelis_adeliae_f            .TF..........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S....
	Pygoscelis_adeliae_y            .T...........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S....
	Spheniscus_humboldti            .T.S.........LIT.......T..................D?DKEVI..--I......S.E..............D.N.I.S....
	Phalacrocorax_sulcirostris      .S.SK.......ALVT.......T..............KI..DHDKEVI..--.......S.E.............AD.N...S....
	Anhinga_novaehollandeae         .L.S.........LVT.......T................T.DHDKEVI.S--.......S.E..............D.N...S....
	Nycticorax_nycticorax           .T.S.A....R..LVT.......A..........M....I..DHDGEVIV.--.......SPEN.V.......D..AD.N...S....
	Chauna_chavaria                 .R...........L.T.T.....T..................DRDKEAV..--......AT.E....NQ....S...D.N...S....
	Anseranas_semipalmata           .R...S.......L.T.D...................A....DHDKEAV..--..E...AT.E....NQ........D.N...S....
	Dendrocygna_arcuata             .RF..........L.T.E...V.................I..D?DKEAV..--......AT.E....N..G......D.N...S....
	Dendrocygna_autumnalis          .RF..........L.T.D.....................I..DHDKEAV..--......AT.E....N..G......D.N...S....
	Dendrocygna_eytoni_d            .RF..........L.T.DVI.V............L....I..DHDKEAV..--....R.DT.E....N..G......D.N...S....
	Dendrocygna_eytoni_e            .RF..........L.T.DVI.V............L....I..DHDKEAV..--..E.R.DT.E....N..G......D.N...S....
	Dendrocygna_viduata             .RFS.........L.T.E...V.................I..D?D?EAV..--......AT.E....N..G.R....D.N...S....
	Coscoroba_coscoroba             ..F..........L.T.D.I...T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S....
	Cygnus_atratus                  .RF..........L.T.D.....T...............I..DHDKEAV..--......ATME....N..G......D.N...S....
	Goose                           .RF..........L.T.D.....T...............I..DHDKEAV..--......ATVE....N..D......D.N...S....
	Anser_indicus                   .RF..........L.T.D.A...T...............I..DHDKEAV..--......ATVE....N..D......D.N...S....
	Branta_canadensis               .RF.......R..L.T.D.....T...............I..DHD???V..--......ATVE....N..G......D.N...S....
	Cereopsis_novaehollandiae       ..F..........L...DVI.T.T...............I..D?D??AV..--......ARME....N..G......D.N...S....
	Chloephaga_picta                .RF..........L.T.E.....T...............I..D??KEAV..--..G...ATME....N..G......D.N...S...E
	Duck                            .RF..........L.T.E...V.T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S...E
	Anas_platyrhynchos              .RF........D.L.T.E...V.T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S...E
	Megapodius_freycinet            .R...........LVTQDV?...T....?....G...??I????????LV.--......ST.EDK..NQ....S...D.N...S....
	Leipoa_ocellata                 IRH..........LVTEDS....T...............I..E?DK??VV.--..G.THAT.ELK..NQ....G..AQ.N...S....
	Ortalis_vetula                  ...........D.LA.EDPNL.......T-.......???????????..PN-...H..ALQEQKI.N..D..S...D.N...S....
	Penelope_jacquacu               ...........D.LA.EDP.........T-.........I..ERDKEA..PN-...H..ALQEQK..N..D..S...D.N...S....
	Penelope_superciliaris          ...........D.LVAEDP....................I..E?DKEA..PN-...H..ALQEQK..N..D..S...D.N...S....
	Bonasa_umbellus                 .RF........V.LV.EDPR...T.A.....M.......I..EHD???L.AS-..E...ATME.R..N..G........N.N.S...T
	Tympanuchus_cupido              .RF........D.LVTED.H...T...............I..EHD???L.AS-..E...ATME.R..N..G........N...S....
	Oreortyx_pictus                 .RF........D.LAT.E.H...T........S......I..EHDTEA..AS-..E...AT.E.R.....A........N...S....
	Callipepla_squamata_n           .RF........D.LAT.E.H...T........Y......I..EHD??A..AS-..E...DT.E.R..N..A........N...S....
	Callipepla_squamata_s           .RF........D.LAT.E.H...T........Y......I..EHD??A..AS-..E...DT.E.R..N..AS.......N...S....
	Lophortyx_californicus          .RF........D.LVT.E.Q...T........Y......I..EHD?EA..AS-..E...AT.E.R..N..A........N...S....
	Colinus_virginianus             .RF........D.LATEE.H...T....MS.MF......T..EHDTEA..AS-..E...AMSE.R..N..V........N...S....
	Cyrtonyx_montezumae_l           .RF........D.LVTEEV....T........S..A.?.I.?E?D???..AS-..E...AT.E.VI.N..G........N...S....
	Cyrtonyx_montezumae_s           .RF........D.LVTEEV....T........S..A.?.I.?E?D???..AS-..E...ATSE.VI.N..G........N...S....
	Alectoris_chukar                ARF..A.....D..VTED.R...T....T-.........I..EHDGETL.A--..E...AT.E.R.....G........N...S....
	Alectoris_rufa                  ARF..A.....D..VTED.H...T....T-.........I..EHD???L.A--..E...AT.E.R.....G........N...S....
	Francolinus_afer                .RF..A....RD..VSEN.R...TH........SM....I..EHDREAP.AS-..E...ATME.RV.NI.G......K.N...S....
	Francolinus_erckelii            .RF..A.....D.AVSEN.R...T...N-.....M....I??EHD?EAP.AS-..E...ATME.RV.NI.G......K.N...S.K..
	Francolinus_coqui_v             .RF..A....RD..VSEN.R...T.........SMN...I..E?D?EA???S-..E...GTME.RV.NI.G......K.N...S....
	Francolinus_coqui_a             .RF..A....RD.AVSEN.R...T.........SMN...I..E?D?EA???S-..E...GTME.RV.NI.G......K.N...S....
	Francolinus_francolinus_a       ARF........V.LDS.D.I...T..LHDS..S...H.KIK.EHDRE????S-..G...ETAEET..N..R........N........
	Francolinus_francolinus_v       .RF........V.LDS.D.I...T..LHDS..S...H.KIK.EHDRE????S-..G...ETAEET..N..R........N........
	Francolinus_pondicerianus       ARFS.A.....D.LVIDDPR.M.T....DS..F.M....I..EHD???LPAS-..E...DTTEER..N..G........N...S....
	Perdix_perdix                   .RF........D.LVTED.Q...T...............I..EHT???L.AS-..E...ATME.R..N..G..D.....N...N....
	Coturnix_delegorguei            .RF........DE.V.DE.RF..T....NH.MF.K....I..EQDGET???S-..E...A.K..RV.N..G........N...NR...
	Coturnix_coturnix_japonica_1    .RF........DE.V.DE.RL..T....NH.MF.K....I..EQDGETL.AS-..E...A.K..RV.N...........N...N....
	Coturnix_coturnix_japonica_2    .RF........DE.V.DE.RL..T....NH.MF.K....I..EQDGETL.AS-..E...A.K..RV.N..G........N...N....
	Arborophilia_torqueola          .RF..S.....V..VKEDPR...T.........H..T??I?.?????????S-....M.ATME.RV.N..G........N...S....
	Bambusicola_thoracica           ARF..A.....V.LDTQE.R...T.......MS......I.IK?DKE?L.AS-..E...ETAEERI.N..G........N....N...
	Tragopan_satyra                 .RF........D.LVTED.H...T...............I..GHDREAL.AS-..E...ATME.R..N..G........N...S....
	Tragopan_temmincki              .RF........D.LVTED.R...T...............I..GHD???L.AS-..E...ATME.R..N..G........N...S....
	Lophophorus_impejanus           .RF..A.....D.LVTED.R...T...............I..EHDREAL.AS-..E...ATME.R..N..G........N...S....
	Crossoptilon_auritum            .RF........D.LVAED.R...T...............I..ERDGEAL.AS-..E...ATME.R..N..G........N...S....
	Lophura_edwardsi                .RF........D.LVAED.R...T.......M.......I..ERDGEAL.AS-..E...ATME.R..N..G........N...S....
	Lophura_ignita                  .RF........D.LVGEDIR...T.......M.......N..ERDGEAL.AS-..E...ATME.R..N.SD........N...S....
	Gallus_gallus                   ARF..ADK...D.LVN.D.R...T....T.D..S..F..I..EHDKETL.AS-..E...DTAEDR..N..G........N...S....
	Grey_jungle_fowl                ARF..ADK...D.LVN.D.R...T....T.D..S..F..I..EHDKETL.AS-..E...DTVEDR..N..G........N...S....
	Phasianus_colchicus             .RF..........LVAED.R.V.T.....S.........I..EHEGEAL.AS-..E...ATME.R..N..G........N...NR..Q
	Syrmaticus_ellioti              .RF..K.....D.LVAED.H...T...............I..ER?G??L.AS-..E...ATME.R..N..G........N...S....
	Syrmaticus_reevesii             .RF..K.......LVAED.H...T.....S.........I..ERNGEAL.AS-..E...ATME.R..N..G........N...SR..E
	Chrysolophus_amherstiae         .RFL.....S.D-LVAED.H...T...............I..EHDG?AL.AS-..E...ATME.R..N..G........N...N....
	Polyplectron_bicalcaratum       .RF....K...D.LA.EEVR...T.....D.S..RD...I..EHDR?????S-..E.Q.TTTEHRVNNE.G......K.N..VS....
	Argusianus_argus_argus          .RF........D.LVSEDRH...T.....H..T......I..EHD?EAL.A--..EH..AT.EDR..N.I...D..L..N...S....
	Pavo_cristatus                  .RF..A.....D.LVSED.H...T.....H.........I..EHDREAL.AS-..E...AT.EHR..N..G........N...S....
	Afropavo_congensis              .RF........D.SAS.D.R...T.....H.........I..EHDGEAL.AS-..E...ATMEQR..N..G........N...S....
	Numida_meleagris                .RF..A.....D.LVTED.R...T......D........I.?????EAL.A--..E...ATME.R..N..D........N...S....
	Acryllium_vulturinum            .RF..A.....D.LVIED.R...T......D........I..EHD???L.A--..E...ATME.R..N..D........N...S....
	Meleagris_gallopavo             .RF........D.LVTED.R...T...H.-.........I..EHDREAL.AS-..E...AT.E.R..N..G........N...S....
	Grus_carunculatus               .T...........LVT.......T..................DHDKEAT..--......AT.E..F...........D.N...S....
	Anthropoides_virgo              .T...........LVT.......T..................DHDKEVT..--......AT.E..F...........D.N...S....
	Grus_vipio                      IT...........LVT.......T..................DHDKEAT..--......AT.E..F...........D.N...S....
	Fulica_atra                     .T...........LVT.....V.TN......S..........DYDKEVT..--..G.Q.AS.E.VF.N.....D..AD.N...S....
	Vanellus_spinosus               .T...........LVT.......T..........L.......DYDKEVI..--......AS................D.N...S..E.
	Larus_rudibundus                .T...........LAT.A...V....................DYDKEDI..--......AS................D.N...S..E.
	Turnix_sylvatica                .RF........DT.AD.D.P.........-.M.......I..EHD??T???S-..E...GMMERL..N..ND.......N...N...E
	Gallirallus_australis           .T.........V.LVT.NI..V.TN...T..S.I...S....DYD???T..??..G.QSA.Q..VF.N........AD.N...S....
	Geococcyx_californianus         .A...A......ALVTTARLH..T....G.....L.H..I..DYNKEVI.S--.N.....S.L....N..G.....AD.N...S....
	Dacelo_novaeguineae             .......D.....LVTE......T.R................EHDKEAI..-Q..EH..AT...RI.......D..MD.N...S....
	Carpococcyx_renauldi            .R...S......GLATT.R....T....G.....L....I..DYD???I..--.......T.ED...NI.H..Y..AH.N..FS....
	Podargus_strigoides             .T.......S...LVDEV.....T..........L.-..I..DRDK??I..--....Q..MG...............D.N...N....
	;
end;

[
begin mrbayes;
	[The following line will let the mcmc chain integrate
	 over the ten fixed amino-acid rate matrices. You can also fix
	 the rates to those in one of the rate matrices.]
	prset aamodelpr=mixed;
end;
]