Optimized ML tree
((((24_O05894MY, (25_RUBR2PS8, 26_RUBR1PS9) 48 ) 47 , (16_RUBRACI5, 17_O05893M3) 49 ) 46 , (((((29_NORVECO1, (30_RUBLRHIg, (31_RUBLBRAJ, (32_HUPJRHOC, (33_RUBRAZO6, (34_RUBRCUP7, 35_P955009P) 59 ) 58 ) 57 ) 56 ) 55 ) 54 , (20_RUBRMET2, (21_P94698D1, (27_RUBRSYN4, 39_O26576M1) 62 ) 61 ) 60 ) 53 , (18_RUBR1ME1, 22_RUBR2ME7) 63 ) 52 , 12_RUBRTHE8) 51 , ((14_RUBRMEG1, 15_O28920AR) 65 , ((36_RUBRPEP7, (43_O29906AR, ((37_O50375ME, 38_RUBHMET1) 70 , (40_O29905A1, (42_O26912M1, 41_O27972A1) 72 ) 71 ) 69 ) 68 ) 67 , (((10_RUBRCLO3, 11_RUBRCLO4) 75 , (7_RUBR2CL5, (8_RUBRPYR6, 9_P96745C8) 77 ) 76 ) 74 , ((5_RUBRBUT5, 6_RUBRHEL6) 79 , (1_RUBRCHL1, ((2_RUBRDES2, (3_RUBRDES3, 4_Q46496DE) 83 ) 82 , (28_RUBRTRE1, (13_O26259ME, 19_RUBR1DE4) 85 ) 84 ) 81 ) 80 ) 78 ) 73 ) 66 ) 64 ) 50 ) 45 , 23_RUBR2PS2) 44 ;

Marginal ML reconstruction
RUBRCHL1          --KYVCSVCGYVYDPADGEPDDPIDPGTGFEDLPEDWVCPVCGVDKDLF----
RUBRDES2          --IYVCTVCGYEYDPAKGDPDSGIKPGTKFEDLPDDWACPVCGASKDAF----
RUBRDES3          --KYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEF----
Q46496DE          --KYVCGVCVYEYDPAKGDPDNGVAPGTAFEDLPADWSCPVCGASKDQF----
RUBRBUT5          --KYVCDICGYVYDPAVGDPDNGVAPGTAFADLPEDWVCPECGVSKDEF----
RUBRHEL6          --KYGCLVCGYVYDPAKGDPDHGIAPGTAFEDLPADWVCPLCGVSKDEF----
RUBR2CL5          --KFICDVCGYIYDPAVGDPDNGVEPGTEFKDIPDDWVCPLCGVDKSQF----
RUBRPYR6          --KWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEF----
P96745C8          --KYICTVCGYIYDEAAGDPDNGVAPGTKFEDIPDDWVCPLCGVPKSDF----
RUBRCLO3          --KYVCTVCGYVYDPEVGDPDNNINPGTSFQDIPEDWVCPLCGVGKDQF----
RUBRCLO4          --KYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQF----
RUBRTHE8          --KWQCTVCGYIYDPEVGDPTQNIPPGTKFEDLPDDWVCPDCGVGKDQF----
O26259ME          --KYVCQMCGYIYDPEEGDPVSGIEAGTPFEDLPDDWVCPVCGVGKDQF----
RUBRMEG1          --KYECSICGYIYDEAEGD-DGNVAAGTKFADLPADWVCPTCGADKDAF----
O28920AR          --KYECQVCGYVYDEAEGDPDNDIPAGTKWEDLPDDWVCPVCGASKDQF----
RUBRACI5          --KYQCIVCGWIYDEAEGWPQDGIAPGTKWEDIPDDWTCPDCGVSKVDF----
O05893M3          --LFRCIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGAAKSDF----
RUBR1ME1          --KYKCKVCGWVYDPLKGDPSQNIPPKTPFEELPDTWICPVCKVGKESF----
RUBR1DE4          --KYVCNVCGYEYDPAEHD-------NVPFDQLPDDWCCPVCGVSKDQF----
RUBRMET2          --RYKCRVCGYIYDPEKGEPRTDTPPGTPFEDLPETWRCPSCGAKKKMF----
P94698D1          --MWRCQTCGYVYDPDRGDKRGKVPPGTRFEDLPDEWRCPICKATKKCF----
RUBR2ME7          --RYQC-MCGWVYDEDKGEPSQNIPPGTKFEDLPDTFRCPQCGLGKNAF----
RUBR2PS2          MKKWICITCGHIYDEALGDEAEGFTPGTRFEDIPDDWCCPDCGATKEDYEEVE
O05894MY          --AYRCPVCDYVYDEANGDAREGFPAGTGWDQIPDDWCCPDCAVRKVDF----
RUBR2PS8          --SYKCPDCNYVYDESAGNVHEGFSPGTPWHLIPEDWCCPDCAVRKLDF----
RUBR1PS9          --RYQCPDCQYIYDENKGEPHEGFHPNTSWNDIPKDWACPDCAVRKVDF----
RUBRSYN4          --NHECRACGYVYIPSQGDQKTSVSPGTPFEALPLNWKCPVCGAPRNYF----
RUBRTRE1          --TYMCDLCGWGYNPEVGDADGGIPAGTAFENLPDHWECPLCGVDKTSF----
NORVECO1          --RMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLGKDVF----
RUBLRHIg          --RMECGICWHVYDPAEGDPVWQIPPGTPFSNLTEDWRCPNCDALQSKF----
RUBLBRAJ          --RLECGICWTVYDPADGDDVAQIAPGTPFAALPEEWHCPNCDAPKSKF----
HUPJRHOC          --IMECKICWTPYDPASGDEFRQVLPGTPFTALPEDWHCPNCDAPKAQF----
RUBRAZO6          --VLECKICWHRYDPAVGDEVWQILAGTPFAALPAHWRCPQCDGDREQF----
RUBRCUP7          --RLECKICWWEYDPEVGDPVWQIAPGTSFSALPAHWRCPNCDGEAEQF----
P955009P          --KLECKICWWVYDPAVGDPVWQIPPGVPFSALPPHWRCPNCDGDADQF----
RUBRPEP7          --KFECTLCGYIYDPALVGPDTPDQDG-AFEDVSENWVCPLCGAGKEDF----
O50375ME          --MYVCRICQYQV------------PDRDFSELGDGWVCPQCGVGRDEF----
RUBHMET1          --MKICRICGYQI------------PEGEFNLLEDGWVCPRCGVGKEEL----
O26576M1          --DFRCTVCNYIFHEE---------ADGEFDSLPADWRCPVCNAPRTAF----
O29905A1          --IYVCPMCGYIVKDETPD------------------VCPLCNAPGESF----
O27972A1          --IYVCPVCGYAMEGEAPE------------------KCPLCNTPKEKF----
O26912M1          --YYVCNWCGNTVEGEAPS------------------RCPICGAPKDEF----
O29906AR          --RWRCKLCGLVFRGDE-------PPE----------VCGRCGATKEQF----
node #44          MKKWICITCGHIYDEALGDEAEGFTPGTRFEDIPDDWCCPDCGATKEDYEEVE
node #45          MKKYQCIVCGYIYDEAEGDPQEGIAPGTKFEDIPDDWTCPDCGASKEDFEEVE
node #46          MKKYQCIVCGYIYDEAEGDPQDGIAPGTKWEDIPDDWTCPDCGASKVDFEEVE
node #47          MKAYQCPVCDYVYDEANGDPHEGFPPGTSWDDIPDDWCCPDCAVRKVDFEEVE
node #48          IKSYQCPDCNYVYDESKGDPHEGFSPGTSWNDIPEDWCCPDCAVRKVDFEEVE
node #49          MKKYQCIVCGYIYDEAEGWPQDGIAPGTKWEDIPDDWTCPDCGASKVDFEEVE
node #50          MKKYQCTVCGYIYDPAEGDPTNNIAPGTKFEDLPDDWVCPDCGASKDQFEEVE
node #51          MKKYQCTVCGYIYDPEEGDPTQNIPPGTKFEDLPDDWVCPDCGAGKDQFEEVE
node #52          IKRYQCRVCGYIYDPEKGDPSQNIPPGTPFEDLPDNWRCPNCGAGKNSFEEVE
node #53          IKRYQCRVCGYIYDPEKGDPSQNIPPGTPFEDLPDNWRCPNCGAGKNSFEEVE
node #54          VKRMQCRVCGYIYDPAKGDPTQNIPPGTPFEDLPDNWRCPNCGAGKNAFEEVE
node #55          VKRMECGICWHVYDPAEGDPVWQIPPGTPFSNLPEDWRCPNCDAPKSKFEEVD
node #56          VKRMECGICWTVYDPAEGDEVRQIPPGTPFAALPEDWHCPNCDAPKSKFEEVD
node #57          VKRMECKICWTVYDPASGDEVRQILPGTPFAALPEDWHCPNCDAPKAQFEEVD
node #58          VKRLECKICWHVYDPAVGDEVWQILPGTPFAALPAHWRCPNCDGDREQFDEVD
node #59          VKRLECKICWWVYDPAVGDPVWQIPPGTPFSALPAHWRCPNCDGDAEQFDEVD
node #60          VKRYKCRVCGYIYDPEKGDPRTNIPPGTPFEDLPDNWRCPSCGASKKTFEEVE
node #61          VKRYKCRVCGYVYDPEKGDQRTNVPPGTPFEDLPDNWRCPVCGASKKSFEEVE
node #62          VKNYKCRVCGYVYDPEKGDQKTNVPPGTPFEALPLNWRCPVCGAPRNSFEEVD
node #63          IKRYQCRVCGWVYDPEKGDPSQNIPPGTPFEDLPDTWRCPQCGAGKNAFEEVE
node #64          MKKYECTVCGYIYDPAEGDPDNNIAPGTKFEDLPDDWVCPLCGASKDQFEEVE
node #65          MKKYECTVCGYIYDEAEGDPDNNIAAGTKFEDLPDDWVCPVCGASKDQFEEVE
node #66          MKKYECTVCGYIYDPAEGDPDNNIAPGTKFEDLPDDWVCPLCGASKDQFEEVE
node #67          MKKYECTVCGYIYDPAEGDPDNNIAPGTKFEDLPDDWVCPLCGASKDQFEEVE
node #68          VKKYRCKICGYVFEGDEGDPDNGIPPEGEFEDLPDGWVCPRCGATKEQFEEVE
node #69          VKMYVCRICGYQIEGEEPDPDDGIPPEGEFNELGDGWVCPRCGAGKEEFEEVD
node #70          VKMYVCRICGYQIEGDEPDPDDGIPPEGEFNELGDGWVCPRCGVGKEEFEEVD
node #71          VKIYVCPVCGYAVEGEAPDPDDGIPPEGEFDELGDGWVCPLCNAPKEKFDEVD
node #72          VKIYVCPVCGYAMEGEAPEPDDGIPPDGDFDDLGDGWKCPLCNTPKEKFDEVD
node #73          MKKYVCTVCGYIYDPAEGDPDNGIAPGTKFEDLPDDWVCPLCGVSKDQFEEVE
node #74          MKKYVCTVCGYIYDPAVGDPDNGVAPGTKFEDIPDDWVCPLCGVSKDQFEEVE
node #75          IKKYVCTVCGYIYDPEVGDPDNGVNPGTNFKDIPDDWVCPLCGVGKDQFEEVE
node #76          MKKYICTVCGYIYDPAVGDPDNGVAPGTKFEDIPDDWVCPLCGVSKSQFEEVE
node #77          IKKYICTVCGYIYDEAAGDPDNGVAPGTKFEDIPDDWVCPLCGVPKSDFEEVE
node #78          MKKYVCTVCGYVYDPAEGDPDNGIAPGTAFEDLPDDWVCPVCGVSKDQFEEVE
node #79          MKKYVCTVCGYVYDPAEGDPDNGIAPGTAFEDLPDDWVCPVCGVSKDEFEEVE
node #80          MKKYVCTVCGYVYDPAEGDPDNGIAPGTAFEDLPDDWVCPVCGVSKDQFEEVE
node #81          MKKYVCTVCGYEYDPAEGDPDNGIAPGTAFEDLPDDWVCPVCGVSKDQFEEVE
node #82          MKKYVCTVCGYEYDPAEGDPDNGIAPGTAFEDLPDDWVCPVCGASKDQFEEVE
node #83          MKKYVCTVCGYEYDPAEGDPDNGVAPGTAFEDLPADWVCPVCGASKDQFEEVE
node #84          MKKYVCNVCGYEYDPAEGDPDNGIAPGTAFEDLPDDWVCPVCGVSKDQFEEVE
node #85          MKKYVCNVCGYEYDPAEGDPDNGIAPGTPFEDLPDDWVCPVCGVSKDQFEEVE

Joint ML reconstruction
RUBRCHL1          --KYVCSVCGYVYDPADGEPDDPIDPGTGFEDLPEDWVCPVCGVDKDLF----
RUBRDES2          --IYVCTVCGYEYDPAKGDPDSGIKPGTKFEDLPDDWACPVCGASKDAF----
RUBRDES3          --KYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEF----
Q46496DE          --KYVCGVCVYEYDPAKGDPDNGVAPGTAFEDLPADWSCPVCGASKDQF----
RUBRBUT5          --KYVCDICGYVYDPAVGDPDNGVAPGTAFADLPEDWVCPECGVSKDEF----
RUBRHEL6          --KYGCLVCGYVYDPAKGDPDHGIAPGTAFEDLPADWVCPLCGVSKDEF----
RUBR2CL5          --KFICDVCGYIYDPAVGDPDNGVEPGTEFKDIPDDWVCPLCGVDKSQF----
RUBRPYR6          --KWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEF----
P96745C8          --KYICTVCGYIYDEAAGDPDNGVAPGTKFEDIPDDWVCPLCGVPKSDF----
RUBRCLO3          --KYVCTVCGYVYDPEVGDPDNNINPGTSFQDIPEDWVCPLCGVGKDQF----
RUBRCLO4          --KYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQF----
RUBRTHE8          --KWQCTVCGYIYDPEVGDPTQNIPPGTKFEDLPDDWVCPDCGVGKDQF----
O26259ME          --KYVCQMCGYIYDPEEGDPVSGIEAGTPFEDLPDDWVCPVCGVGKDQF----
RUBRMEG1          --KYECSICGYIYDEAEGD-DGNVAAGTKFADLPADWVCPTCGADKDAF----
O28920AR          --KYECQVCGYVYDEAEGDPDNDIPAGTKWEDLPDDWVCPVCGASKDQF----
RUBRACI5          --KYQCIVCGWIYDEAEGWPQDGIAPGTKWEDIPDDWTCPDCGVSKVDF----
O05893M3          --LFRCIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGAAKSDF----
RUBR1ME1          --KYKCKVCGWVYDPLKGDPSQNIPPKTPFEELPDTWICPVCKVGKESF----
RUBR1DE4          --KYVCNVCGYEYDPAEHD-------NVPFDQLPDDWCCPVCGVSKDQF----
RUBRMET2          --RYKCRVCGYIYDPEKGEPRTDTPPGTPFEDLPETWRCPSCGAKKKMF----
P94698D1          --MWRCQTCGYVYDPDRGDKRGKVPPGTRFEDLPDEWRCPICKATKKCF----
RUBR2ME7          --RYQC-MCGWVYDEDKGEPSQNIPPGTKFEDLPDTFRCPQCGLGKNAF----
RUBR2PS2          MKKWICITCGHIYDEALGDEAEGFTPGTRFEDIPDDWCCPDCGATKEDYEEVE
O05894MY          --AYRCPVCDYVYDEANGDAREGFPAGTGWDQIPDDWCCPDCAVRKVDF----
RUBR2PS8          --SYKCPDCNYVYDESAGNVHEGFSPGTPWHLIPEDWCCPDCAVRKLDF----
RUBR1PS9          --RYQCPDCQYIYDENKGEPHEGFHPNTSWNDIPKDWACPDCAVRKVDF----
RUBRSYN4          --NHECRACGYVYIPSQGDQKTSVSPGTPFEALPLNWKCPVCGAPRNYF----
RUBRTRE1          --TYMCDLCGWGYNPEVGDADGGIPAGTAFENLPDHWECPLCGVDKTSF----
NORVECO1          --RMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLGKDVF----
RUBLRHIg          --RMECGICWHVYDPAEGDPVWQIPPGTPFSNLTEDWRCPNCDALQSKF----
RUBLBRAJ          --RLECGICWTVYDPADGDDVAQIAPGTPFAALPEEWHCPNCDAPKSKF----
HUPJRHOC          --IMECKICWTPYDPASGDEFRQVLPGTPFTALPEDWHCPNCDAPKAQF----
RUBRAZO6          --VLECKICWHRYDPAVGDEVWQILAGTPFAALPAHWRCPQCDGDREQF----
RUBRCUP7          --RLECKICWWEYDPEVGDPVWQIAPGTSFSALPAHWRCPNCDGEAEQF----
P955009P          --KLECKICWWVYDPAVGDPVWQIPPGVPFSALPPHWRCPNCDGDADQF----
RUBRPEP7          --KFECTLCGYIYDPALVGPDTPDQDG-AFEDVSENWVCPLCGAGKEDF----
O50375ME          --MYVCRICQYQV------------PDRDFSELGDGWVCPQCGVGRDEF----
RUBHMET1          --MKICRICGYQI------------PEGEFNLLEDGWVCPRCGVGKEEL----
O26576M1          --DFRCTVCNYIFHEE---------ADGEFDSLPADWRCPVCNAPRTAF----
O29905A1          --IYVCPMCGYIVKDETPD------------------VCPLCNAPGESF----
O27972A1          --IYVCPVCGYAMEGEAPE------------------KCPLCNTPKEKF----
O26912M1          --YYVCNWCGNTVEGEAPS------------------RCPICGAPKDEF----
O29906AR          --RWRCKLCGLVFRGDE-------PPE----------VCGRCGATKEQF----
node #44          MKKWICITCGHIYDEALGDEAEGFTPGTRFEDIPDDWCCPDCGATKEDYEEVE
node #45          CKKYQCIVCGYIYDEAEGDPTEGIAPGTKFEDIPDDWCCPDCGASKEDFEEVD
node #46          CKKYQCIVCGYIYDEAEGDPQEGIAPGTKWEDIPDDWCCPDCGASKVDFEEVD
node #47          CKRYQCPVCNYVYDEAKGDPHEGFSPGTSWDDIPDDWCCPDCAVRKVDFEEVD
node #48          CKRYQCPDCNYVYDESKGDPHEGFSPGTSWNDIPEDWCCPDCAVRKVDFEEVD
node #49          CKKYQCIVCGYIYDEAEGWPQDGIAPGTKWEDIPDDWTCPDCGASKVDFEEVD
node #50          CKKYQCTVCGYIYDPAEGDPTQGIAPGTKFEDLPDDWVCPDCGASKDQFEEVD
node #51          CKKYQCTVCGYIYDPEEGDPTQNIPPGTKFEDLPDDWVCPDCGAGKDQFEEVD
node #52          CKRYQCRVCGYVYDPEKGDPTQNIPPGTPFEDLPDNWRCPECGAGKNAFEEVD
node #53          CKRYQCRVCGYVYDPEKGDPTQNIPPGTPFEDLPDNWRCPECGAGKNAFEEVD
node #54          CKRMQCRVCGYVYDPAKGDPTQNIPPGTPFADLPDNWRCPECGAGKNAFEEVD
node #55          CKRMECGICWHVYDPAEGDPVWQIPPGTPFANLPEDWRCPNCDAPKSKFEEVD
node #56          CKRMECGICWHVYDPAEGDEVWQIPPGTPFAALPEDWHCPNCDAPKSKFEEVD
node #57          CKRMECKICWHVYDPAEGDEVWQIPPGTPFAALPEDWHCPNCDAPKAQFEEVD
node #58          CKRLECKICWHVYDPAVGDEVWQIPPGTPFAALPAHWRCPNCDGDREQFEEVD
node #59          CKRLECKICWWVYDPAVGDPVWQIPPGTPFSALPAHWRCPNCDGDAEQFEEVD
node #60          CKRYKCRVCGYVYDPEKGDPRTNVPPGTPFEDLPDNWRCPVCGASKNAFEEVD
node #61          CKRYKCRVCGYVYDPEKGDQRTNVPPGTPFEDLPDNWRCPVCGASKNAFEEVD
node #62          CKNYKCRVCGYVYDPEKGDQRTNVPPGTPFEALPDNWRCPVCGAPKNAFEEVD
node #63          CKRYQCRVCGWVYDPEKGDPTQNIPPGTPFEDLPDTWRCPECGAGKNAFEEVD
node #64          CKKYECTVCGYIYDPAEGDPDNGIAPGTKFEDLPDDWVCPVCGASKDQFEEVD
node #65          CKKYECTVCGYIYDEAEGDPDNDIAAGTKFEDLPDDWVCPVCGASKDQFEEVD
node #66          CKKYECTVCGYIYDPAEGDPDNGIAPGTKFEDLPDDWVCPVCGASKDQFEEVD
node #67          CKKYECTVCGYIYDPAEGDPDNGIAPGTKFEDLPDDWVCPVCGASKDQFEEVD
node #68          CKKYECRICGYVFEGDEPDPDDGIPPEGEFDELGDGWVCPRCGAGKEQFEEVD
node #69          CKMYVCRICGYVVEGDEPDPDDGIPPEGEFDELGDGWVCPRCGAGKEEFEEVD
node #70          CKMYVCRICGYQVEGDEPDPDDGIPPEGEFNELGDGWVCPRCGVGKEEFEEVD
node #71          CKIYVCPVCGYVVEGEAPDPDDGIPPEGEFDELGDGWVCPLCNAPKEKFEEVD
node #72          CKIYVCPVCGYAMEGEAPEPDDGIPPEGEFDELGDGWKCPLCNTPKEKFEEVD
node #73          CKKYVCTVCGYIYDPAEGDPDNGIAPGTKFEDLPDDWVCPVCGVSKDQFEEVD
node #74          CKKYVCTVCGYIYDPAVGDPDNGVAPGTKFEDIPDDWVCPLCGVSKDQFEEVD
node #75          CKKYVCTVCGYIYDPEVGDPDNGVNPGTNFQDIPDDWVCPLCGVGKDQFEEVD
node #76          CKKYICTVCGYIYDPAVGDPDNGVAPGTKFEDIPDDWVCPLCGVSKSQFEEVD
node #77          CKKYICTVCGYIYDEAAGDPDNGVAPGTKFEDIPDDWVCPLCGVPKSDFEEVD
node #78          CKKYVCTVCGYVYDPAEGDPDNGIAPGTAFEDLPDDWVCPVCGVSKDQFEEVD
node #79          CKKYVCTVCGYVYDPAEGDPDNGIAPGTAFEDLPDDWVCPVCGVSKDEFEEVD
node #80          CKKYVCTVCGYVYDPAEGDPDNGIAPGTAFEDLPDDWVCPVCGVSKDQFEEVD
node #81          CKKYVCTVCGYEYDPAEGDPDNGIAPGTAFEDLPDDWVCPVCGVSKDQFEEVD
node #82          CKKYVCTVCGYEYDPAEGDPDNGIAPGTAFEDLPDDWVCPVCGASKDQFEEVD
node #83          CKKYVCTVCGYEYDPAEGDPDNGVAPGTAFEDLPADWVCPVCGASKDQFEEVD
node #84          CKKYVCTVCGYEYDPAEGDPDNGIAPGTAFEDLPDDWVCPVCGVSKDQFEEVD
node #85          CKKYVCTVCGYEYDPAEGDPDNGIAPGTPFEDLPDDWVCPVCGVSKDQFEEVD


