#NEXUS begin data; dimensions ntax=12 nchar=128; format datatype=protein missing=? gap=- interleave=yes; matrix A.tenuis AFIMIFFLVMPVMIGGFGNWLVPLYIGAPDMAFPRLNNISFWLLPPALILLLGSAFVEQG Porites AFIMIFFLVMPVMIGGFGNWLIPLYIGAPDMAFPRLNNISFWLLPPALILLLGSAFVEQG Nematostella AFLMIFFLVMPVMMGGFGNWFVPLYIGAPDMAFPRLNNISFWLLPPALILLLGSAFVEQG Metridium AFIMIFFLVMPVMIGGFGNWLVPLYIGAPDMAFPRLNNISFWLLPPALILLLGSAFVEQG M.alcicornis AFVMIFFLVMPVLIGGFGNWFVPLYIGAPDMAFPRLNNLSFWLLPPALLLLLGSSLVEQG Leiopathes ALIMIFFLVMPVMIGGFGNWLVPLYIGAPDMAFPRLNNISFWLLPPALILLLGSSFVEQG Hydra AFVMIFFLVMPVLIGGYGNWFVPIYIGAPDMAFPRLNNLSFWLLPPALILLLTSSLVEQG E.tourneforti ALLMIFFLVMPVMIGGFGNWFVPIMIGAPDMAFPRLNNISFWLLPPSLILLVGSMFVEQG Corynactis AFVMIFFLVMPVMIGGFGNWLVPLYIGAPDMAFPRLNNISFWLLPPALILLLGSAFVEQG C.elegans AILMIFFMVMPTMIGGFGNWLLPLMLGAPDMSFPRLNNLSFWLLPTSMLLILDACFVDMG Bathypathes ALIMIFFLVMPVMIGGFGNWLVPLYIGAPDMAFPRLNNISFWLLPPALILLLGSSFVEQG Amplexidiscus AFIMIFFLVMPVMIGGFGNWLVPLYIGAPDMAFPRLNNISFWLLPPALILLLGSAFVEQG A.tenuis VGTGWTVYPPLSSIQAHSGGAVDMAIFSLHLAGVSSILGAMNFITTILNMRAPGMTLNKM Porites AGTGWTVYPPLSSIQAHSGGAVDMAIFSLHLAGVSSILGAMNFITTIFNMRAPGLTLNRM Nematostella VGTGWTMYPPLASIQTHSGGAVDMAIFSLHLAGASSILGSMNFITTVFNMRAPGVTMDRL Metridium VGTGWTVYPPLSAIQAHSGGAVDMAIFSLHLAGASSILGAMNFITTIFNMRAPGMTMDRL M.alcicornis AGTGWTVYPPLSGPQTHSGGSVDLAIFSLHCAGASSIMGAINFITTIFNMRAPGMTMDKM Leiopathes VGAGWTIYPPLSSIQAHSGGAVDMAIFSLHLAGASSILGAMNFITTISNMRAPGVTMDRL Hydra AGTGWTVYPPLSGSLAHSGGSVDLAIFSLHCAGFSSIAGAINFITTIFNMRTPGLTFDKL E.tourneforti AGTGWTIYPPLSSIQAHSGGAVDMAIFSLHLAGISSILSSINFITTIINMRVPGMSMHRL Corynactis VGTGWTVYPPLSNIQAHSGGAVDMAIFSLHLAGASSILGAINFITTIFNMRAPGVTLDRM C.elegans CGTSWTVYPPLSTM-GHPGSSVDLAIFSLHAAGLSSILGGINFMCTTKNLRSSSISLEHM Bathypathes VGAGWTIYPPLSSIQAHSGGAVDMAIFSLHLAGASSILGAMNFITTIFNMRAPGVTMDRL Amplexidiscus VGTGWTGLSPLSNIQAHSGGAVDMAIFSLHLAGASSILGAMNFITTILNMRAPGVTLDRM A.tenuis PLFVWSIL Porites PLFVWSIL Nematostella PLFVWSVL Metridium PLFVWSIL M.alcicornis PLFVWSVL Leiopathes PLFVWSIL Hydra PLFVWSVL E.tourneforti PLFVWSVL Corynactis PLFVWSIL C.elegans TLFVWTVF Bathypathes PLFVWSIL Amplexidiscus PLFVWSIL ; end; begin mrbayes; log start filename=CnidarianProtein.log replace; lset rates=gamma; prset aamodelpr=mixed; mcmcp ngen=500000 samplefreq=100 nchains=4 savebrlens=yes filename=Cnidaria; outgroup C.elegans; mcmc; end;