Difference between revisions of "Reference tree for APSES domains"
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;How this tree was computed: | ;How this tree was computed: | ||
| − | The input sequence alignment was derived from the [[Reference alignment for APSES | + | The input sequence alignment was derived from the [[Reference alignment for APSES domains (MUSCLE, reference species)| APSES domains - MUSCLE aligned and sequence names revised]] file based on the MSA from Assignment 3. The PHYLIP input file is given in the [[Assignment_5_fallback_data|Fallback data page]]. Columns that represented regions of uncertain alignment were deleted, as well as large gapped sections. Using the PHYLIP suite online, at the Institut Pasteur, as described in the instructions, the following tree was constructedas a UPGMA NJ tree . |
The program '''retree'' was used on the output treefile to rotate particular subclades around their branchpoint. This was done to arrange the species within a clade as nearly as possible to correspond to in the reference cladogram. While this is a "cosmetic" change (rotations around branch points do not change the topology of a tree), it facilitates analysis, especially to evaluate how many species are present in each clade and which species may be missing. | The program '''retree'' was used on the output treefile to rotate particular subclades around their branchpoint. This was done to arrange the species within a clade as nearly as possible to correspond to in the reference cladogram. While this is a "cosmetic" change (rotations around branch points do not change the topology of a tree), it facilitates analysis, especially to evaluate how many species are present in each clade and which species may be missing. | ||
Revision as of 18:11, 1 December 2014
- How this tree was computed
The input sequence alignment was derived from the APSES domains - MUSCLE aligned and sequence names revised file based on the MSA from Assignment 3. The PHYLIP input file is given in the Fallback data page. Columns that represented regions of uncertain alignment were deleted, as well as large gapped sections. Using the PHYLIP suite online, at the Institut Pasteur, as described in the instructions, the following tree was constructedas a UPGMA NJ tree .
The program 'retree was used on the output treefile to rotate particular subclades around their branchpoint. This was done to arrange the species within a clade as nearly as possible to correspond to in the reference cladogram. While this is a "cosmetic" change (rotations around branch points do not change the topology of a tree), it facilitates analysis, especially to evaluate how many species are present in each clade and which species may be missing.
The APSES Domain Reference Tree
,---13:Mbp1 NEUCR
!
,---85 ,-12:Mbp1 MAGGR
! ! ,-89
! ! ! `-11:Mbp1 GIBZE
! `-86
! ! ,-10:Mbp1 ASPNI
! `-87
! ! ,--9:Mbp1 ASPTE
,-84 `-88
! ! `--8:Mbp1 ASPFU
! !
! ! ,-14:Mbp1 COPCI
! ! ,--92
! ! ,-91 `-15:MbpA CRYNE
,-83 ! ! !
! ! `-90 `-----16:Mbp1 SCHPO
! ! !
! ! `------17:Mbp1 USTMA
! !
! ! ,------19:Mbp1 YARLI
! `-93
,-76 `------18:Mbp1 CRYNE
! !
! ! ,--2:Mbp1 CANGL
! ! ,-79
! ! ! `--1:Mbp1 SACCE
! ! ,---78
! ! ! ! ,--3:Mbp1 ASHGO
! ! ! `-80
! `-77 `--4:Mbp1 KLULA
! !
! ! ,--7:Mbp1 PICST
! ! ,-82
! `------81 `--6:Mbp1 DEBHA
,-75 !
! ! `--5:Mbp1 CANAL
! !
! ! ,----28:MbpA NEUCR
! ! ,100
! ! ! ! ,-27:MbpA MAGGR
! ! ! `101
! ! ! `-26:MbpA GIBZE
! ! ,--96
! ! ! ! ,-24:MbpA ASPTE
! ! ! ! ,-----98
! ! ! ! ! ! ,-23:MbpA ASPNI
! ! ! `-97 `-99
! `-94 ! `-22:MbpA ASPFU
,-----------------74 ! !
! ! ! `-----25:MbpA YARLI
! ! !
! ! ! ,---------21:MbpB USTMA
! ! `-95
! ! `---------20:MbpA SCHPO
! !
! ! ,-----31:Swi4 CANGL
! ! ,104
! ! ! ! ,---30:Swi4 SACCE
! ! ,-103 `105
! ! ! ! `---29:Swi4 ASHGO
! ! ! !
! ! ! `--------32:Swi4 KLULA
! `-102
! ! ,-35:MbpA PICST
! ! ,107
! `--------106 `-34:MbpA DEBHA
! !
! `-33:MbpA CANAL
!
! ,-50:Sok2 MAGGR
! ,123
,---73 ! `-49:Sok2 GIBZE
! ! !
! ! ,119 ,-46:Sok2 ASPNI
! ! ! ! ,122
! ! ! ! ,121 `-45:Sok2 ASPFU
! ! ! ! ! !
! ! ,118 `120 `-47:Sok2 ASPTE
! ! ! ! !
! ! ! ! `-48:SokA ASPNI
! ! ! !
! ! ! `-51:SokA YARLI
! ! !
! ! ! ,--42:Sok2 CANGL
! ! ! !
! ! ! ! ,-37:Sok2 SACCE
! ! ,-109 ,112 ,115
! ! ! ! ! ! ,114 `-36:Sok2 ASHGO
! ! ! ! ! ! ! !
! ! ! ! ! ! ! `-38:Sok2 KLULA
! ! ! ! ! `113
,-----72 ! ! ! ,111 ! ,-41:Sok2 PICST
! ! ! ! ! ! ! ! ,117
! ! ! ! ! ! ! `116 `-40:Sok2 DEBHA
! ! `-------------------------108 ! ! ! !
! ! ! `110 ! `-39:Phd1 CANAL
! ! ! ! !
! ! ! ! `--43:Phd1 SACCE
! ! ! !
! ! ! `--44:Sok2 YARLI
! ! !
! ! ! ,------55:SokA CANGL
! ! `124
! ! ! ,-54:SokA DEBHA
! ! `--125
! ! ! ,-53:SokA PICST
! ! `126
! ! `-52:Sok2 CANAL
-71 !
! ! ,-----------56:MbpC CANAL
! ! ,-----------------128
! `------127 `-----------57:MbpB DEBHA
! !
! `-------------------------------58:MbpB SCHPO
!
! ,----64:Xbp1 MAGGR
! ,----134
! ! `----63:Xbp1 GIBZE
! ,--------------------130
! ! ! ,-------62:XbpA ASPNI
! ! `-131
! ! ! ,----61:Xbp1 ASPTE
! ! `132
! ! ! ,-60:Xbp1 ASPNI
! ! `--133
`----------129 `-59:Xbp1 ASPFU
!
! ,-----------------------69:Xbp1 SACCE
! !
! ,136 ,---66:Xbp1 DEBHA
! ! ! ,-------138
! ! ! ! `---65:Xbp1 CANAL
! ! `-------137
`-----135 ! ,----------68:Xbp1 YARLI
! `139
! `----------67:Xbp1 COPCI
!
`--------------------------70:Xbp1 USTMA
PHYLIP Tree File
(((((((((Mbp1_NEUCR:0.12887,((Mbp1_MAGGR:0.08575,Mbp1_GIBZE:0.08575):0.01322, (Mbp1_ASPNI:0.04245,(Mbp1_ASPTE:0.01625,Mbp1_ASPFU:0.01625):0.0262):0.05652):0.0299):0.10027, (((Mbp1_COPCI:0.08125,MbpA_CRYNE:0.08125):0.08562,Mbp1_SCHPO:0.16687):0.01938, Mbp1_USTMA:0.18625):0.04289):0.02119,(Mbp1_YARLI:0.19385,Mbp1_CRYNE:0.19385):0.05649):0.0563, (((Mbp1_CANGL:0.06605,Mbp1_SACCE:0.06605):0.04984,(Mbp1_ASHGO:0.08655, Mbp1_KLULA:0.08655):0.02934):0.10725,((Mbp1_PICST:0.03550,Mbp1_DEBHA:0.03550):0.02163, Mbp1_CANAL:0.05713):0.16602):0.08349):0.03608,(((MbpA_NEUCR:0.13598, (MbpA_MAGGR:0.07465,MbpA_GIBZE:0.07465):0.06133):0.04315,((MbpA_ASPTE:0.0083, (MbpA_ASPNI:0.0,MbpA_ASPFU:0.0):0.0083):0.1645,MbpA_YARLI:0.1728):0.00632):0.10305, (MbpB_USTMA:0.2437,MbpA_SCHPO:0.2437):0.03847):0.06055):0.0634,(((Swi4_CANGL:0.16035, (Swi4_SACCE:0.12425,Swi4_ASHGO:0.12425):0.0361):0.06113,Swi4_KLULA:0.22148):0.10572, ((MbpA_PICST:0.06255,MbpA_DEBHA:0.06255):0.01428,MbpA_CANAL:0.07683):0.25038):0.0789):0.42038, (((((Sok2_MAGGR:0.01605,Sok2_GIBZE:0.01605):0.01462,(((Sok2_ASPNI:0.0, Sok2_ASPFU:0.0):0.00805,Sok2_ASPTE:0.00805):0.01688,SokA_ASPNI:0.02493):0.00574):0.04416, SokA_YARLI:0.07483):0.04186,(((Sok2_CANGL:0.08693,(((Sok2_SACCE:0.0489, Sok2_ASHGO:0.0489):0.0079,Sok2_KLULA:0.0568):0.00698,((Sok2_PICST:0.0, Sok2_DEBHA:0.0):0.01605,Phd1_CANAL:0.01605):0.04773):0.02315):0.00887, Phd1_SACCE:0.09581):0.00666,Sok2_YARLI:0.10246):0.01423):0.08975,(SokA_CANGL:0.18773, (SokA_DEBHA:0.08588,(SokA_PICST:0.05025,Sok2_CANAL:0.05025):0.03563):0.10186):0.01871):0.62005):0.11528, ((MbpC_CANAL:0.28905,MbpB_DEBHA:0.28905):0.45758,MbpB_SCHPO:0.74662):0.19515):0.15737, (((Xbp1_MAGGR:0.14705,Xbp1_GIBZE:0.14705):0.15829,(XbpA_ASPNI:0.20350, (Xbp1_ASPTE:0.14,(Xbp1_ASPNI:0.0269,Xbp1_ASPFU:0.0269):0.1131):0.0635):0.10184):0.49999, ((Xbp1_SACCE:0.56026,((Xbp1_DEBHA:0.12385,Xbp1_CANAL:0.12385):0.22894, (Xbp1_YARLI:0.28015,Xbp1_COPCI:0.28015):0.07264):0.20747):0.07706, Xbp1_USTMA:0.63732):0.16802):0.2938);
