Difference between revisions of "Reference tree for APSES domains"
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| + | <div id="BIO"> | ||
| + | <div class="b1"> | ||
| + | APSES domain reference tree | ||
| + | </div> | ||
| + | |||
| + | |||
| + | <section begin=contents_summary /> | ||
| + | A phylogentic tree for all APSES domains found in the reference fungi. | ||
| + | <section end=contents_summary /> | ||
| + | |||
| + | |||
| + | __TOC__ | ||
| + | |||
| + | |||
| + | ==Data and methods== | ||
| + | |||
| + | The input sequence alignment was derived from the [[Reference alignment for KilA-N domains (MUSCLE, reference species)| KilA-N 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. | ||
| + | <!-- From the (deleted) 2006 version: | ||
;How this tree was computed: | ;How this tree was computed: | ||
| − | + | Based on the notion that the Mbp1 clade that came out of the reference phylogenetic tree needed to be reviewed, the following steps were performed. | |
| + | |||
| + | # Edited a multi-FASTA file to comprise only the 32 sequences from the polyphyletic clade that contains all the Mbp1 genes | ||
| + | # Performed a T-Coffee alignment with default parameters with these sequences | ||
| + | # Edited the resulting MSA into a valid PHYLIP input file (reduce large gapped stretches to two characters each, remove uncertain regions, shave frayed ends). | ||
| + | # Ran promlk with default parameters plus global rearrangements | ||
| + | # Manually rearranged the output tree using '''retree''' to correspond as closely as possible to the order in the reference cladogram of fungi | ||
| + | | ||
| + | | ||
| + | |||
| + | Add: input phylip file; bootstrapping... | ||
| + | |||
| + | |||
| + | --> | ||
| + | |||
| − | |||
| − | |||
==The APSES Domain Reference Tree== | ==The APSES Domain Reference Tree== | ||
| Line 177: | Line 209: | ||
(Xbp1_YARLI:0.28015,Xbp1_COPCI:0.28015):0.07264):0.20747):0.07706, | (Xbp1_YARLI:0.28015,Xbp1_COPCI:0.28015):0.07264):0.20747):0.07706, | ||
Xbp1_USTMA:0.63732):0.16802):0.2938); | Xbp1_USTMA:0.63732):0.16802):0.2938); | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | | ||
| + | ==Notes== | ||
| + | <references /> | ||
| + | |||
| + | |||
| + | | ||
| + | |||
| + | |||
| + | [[Category:Bioinformatics]] | ||
| + | |||
| + | </div> | ||
Latest revision as of 16:04, 26 September 2015
APSES domain reference tree
A phylogentic tree for all APSES domains found in the reference fungi.
Data and methods
The input sequence alignment was derived from the KilA-N 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);
Notes
