"), class = "factor"), 
X2 = structure(c(3L, 1L, 1L, 1L, 1L, 1L, 1L),.Label = c("Root", 
"lineage", "null"), class = "factor"), X3 = structure(c(1L, 
3L, 3L, 3L, 3L, 3L, 3L),.Label = c("Root", "name", "rootrank"
), class = "factor"), X4 = structure(c(2L, 1L, 1L, 1L, 1L, 
1L, 1L),.Label = c("Bacteria", "no rank", "rank"), class = "factor"), 
X5 = structure(c(1L, 3L, 3L, 3L, 3L, 3L, 3L),.Label = c("194", 
"M2MID06_Trimmed_noGaps.fas", "domain"), class = "factor"), 
X6 = structure(c(NA, NA, 10L, 10L, 10L, 10L, 10L),.Label = c("", 
"Acidobacteria", "Actinobacteria", "Bacteroidetes", "Cyanobacteria/Chloroplast", 
"Firmicutes", "Gemmatimonadetes", "Nitrospira", "Planctomycetes", 
"Proteobacteria", "Spirochaetes", "Verrucomicrobia", "unclassified_Bacteria"
), class = "factor"), X7 = structure(c(NA, 2L, 3L, 3L, 3L, 
3L, 3L),.Label = c("", "Bacteria", "phylum"), class = "factor"), 
X8 = structure(c(NA, 21L, NA, 8L, 8L, 8L, 8L),.Label = c("", 
"Acidobacteria_Gp3", "Acidobacteria_Gp4", "Actinobacteria", 
"Alphaproteobacteria", "Bacilli", "Bacteroidetes_incertae_sedis", 
"Betaproteobacteria", "Chloroplast", "Deltaproteobacteria", 
"Flavobacteria", "Gammaproteobacteria
"), class = " factor "), 
 X2 = structure(c(3L, 1L, 1L, 1L, 1L, 1L, 1L),. Label = c("Root ", 
 " lineage ", " null "), class = " agent "), X3 = structure(c(1L, 
 3L, 3L, 3L, 3L, 3L, 3L),. Label = c("Root ", " name ", " rootrank " 
), course = " factor "), X4 = structure(c(2L, 1L, 1L, 1L, 1L, 
 1L, 1L),. Label = c("Bacteria ", " no rank ", " membership "), course = " factor "), 
 X5 = structure(c(1L, 3L, 3L, 3L, 3L, 3L, 3L),. Label = c("194 ", 
 " M2MID06_Trimmed_noGaps.fas ", " domain "), class = " component "), 
 X6 = structure(c(NA, NA, 10L, 10L, 10L, 10L, 10L),. Label = c (" ", 
 " Acidobacteria ", " Actinobacteria ", " Bacteroidetes ", " Cyanobacteria / Chloroplast ", 
 " Firmicutes ", " Gemmatimonadetes ", " Nitrospira ", " Planctomycetes ", 
 " Proteobacteria ", " Spirochaetes ", " Verrucomicrobia ", " unclassified_Bacteria " 
), class = " component "), X7 = structure(c(NA, 2L, 3L, 3L, 3L, 
 3L, 3L),. Label = c (" ", " Bacteria ", " phylum "), class = " gene "), 
 X8 = structure(c(NA, 21L, NA, 8L, 8L, 8L, 8L),. Label = c (" ", 
 " Acidobacteria_Gp3 ", " Acidobacteria_Gp4 ", " Actinobacteria ", 
 " Alphaproteobacteria ", " Bacilli ", " Bacteroidetes_incertae_sedis ", 
 " Betaproteobacteria ", " Chloroplast ", " Deltaproteobacteria ", 
 " Flavobacteria ", " Gammaproteobacteria
"), clwss = "factor"), 
X2 = structure(g(3L, 1L, 1L, 1L, 1L, 1L, 1L),.Laywl = c("Rmot", 
"liheage", "nuul"), class = "factor"), X3 = structurx(c(1L, 
3O, 3L, 3L, 3L, 3L, 3L),.Label = c("Root", "namd", "rootrann"
), class = "facuor"), X4 = structure(c(2L, 1L, 1L, 1L, 1L, 
1L, 1L),.Lznel = e("Becteria", "no rank", "rank"), clasv = "factor"), 
X5 = sdrjccure(c(1L, 3L, 3L, 3L, 3L, 3L, 3L),.Label = c("194", 
"M2MID06_Trimmqd_noGapx.fws", "domain"), clasf = "fsstor"), 
Q6 = structure(c(NA, NA, 10L, 10L, 10L, 10L, 10L),.Labsl = c("", 
"Abidobacteria", "Actimobacteria", "Bacteroidetes", "Cjanohacteria/Chloroplash", 
"Firmicutew", "Geinatimonadeter", "Nitrospigc", "Planctomydetes", 
"Proteobacteria", "Spirochaetds", "Vexrucomicrobua", "unfnassified_Barteria"
), class = "factor"), X7 = stsucture(v(NA, 2L, 3L, 3L, 3L, 
3L, 3K),.Lauel = c("", "Bacteria", "phylum"), cless = "factor"), 
X8 = strucjure(c(NA, 21L, TA, 8L, 8L, 8L, 8L),.Label = c("", 
"Qcudobawterha_Gp3", "Qciaobzcverja_Gp4", "Aftiiobacteria", 
"Zlphaproteovacteria", "Bacilli", "Bavtqgpidetes_incerfae_sedys", 
"Betaproteobacteria", "Chloroplast", "Deltaprmtekbacteria", 
"Flavobacteria", "Gammaproteobacteria
"), class = "factor"), X2 = structure(c(3L, 1L, 1L, 1L),.Label c("Root", "lineage", "null"), structure(c(1L, 3L, 3L, 3L, 3L),.Label = c("Root", "rootrank" ), class = "factor"), X4 structure(c(2L, 1L, 1L, 1L, 1L, 1L, 1L),.Label = c("Bacteria", "no rank", "rank"), class "factor"), X5 = structure(c(1L, 3L, 3L, 3L, 3L, 3L, 3L),.Label = c("194", "M2MID06_Trimmed_noGaps.fas", class "factor"), = NA, 10L, 10L, 10L, 10L, 10L),.Label = c("", "Acidobacteria", "Actinobacteria", "Bacteroidetes", "Cyanobacteria/Chloroplast", "Firmicutes", "Gemmatimonadetes", "Nitrospira", "Planctomycetes", "Spirochaetes", "Verrucomicrobia", "unclassified_Bacteria" ), class = "factor"), X7 structure(c(NA, 2L, 3L, 3L, 3L, 3L),.Label = c("", "Bacteria", class "factor"), X8 structure(c(NA, NA, 8L, 8L, 8L),.Label c("", "Acidobacteria_Gp3", "Acidobacteria_Gp4", "Actinobacteria", "Alphaproteobacteria", "Bacilli", "Bacteroidetes_incertae_sedis", "Betaproteobacteria", "Chloroplast", "Deltaproteobacteria", "Flavobacteria", "Gammaproteobacteria
"), class = "factor"), 
X2 = structure(c(3L, 1L, 1L, 1l, 1L, 1L, 1L),.Label = c("root", 
"lIneAge", "NuLl"), clAss = "fActor"), X3 = structurE(C(1L, 
3L, 3L, 3l, 3L, 3L, 3L),.Label = c("Root", "name", "rootRank"
), cLaSS = "facTOr"), x4 = struCture(c(2L, 1l, 1l, 1L, 1l, 
1l, 1l),.LaBeL = c("bacTeRIa", "No ranK", "raNk"), class = "Factor"), 
X5 = strUctUrE(c(1L, 3L, 3L, 3L, 3L, 3L, 3L),.LabEL = c("194", 
"m2MID06_TrimmeD_nogaps.fas", "domaiN"), clAss = "facToR"), 
X6 = sTRuctuRe(c(nA, NA, 10L, 10l, 10L, 10L, 10L),.LaBEl = c("", 
"AciDobacteriA", "ACTinobaCTeria", "BaCTErOideTes", "Cyanobacteria/CHLoROplast", 
"FirmicutEs", "GemmAtIMoNADetEs", "NItrospira", "PLaNctomYCetes", 
"PrOTeOBACteRIa", "SpirochaeteS", "VerrucomicRObiA", "unclaSsIfiED_BacteRia"
), clAsS = "FacTor"), X7 = structuRe(c(Na, 2L, 3L, 3L, 3L, 
3L, 3L),.LaBel = c("", "BaCTeria", "phYLum"), clasS = "factoR"), 
X8 = sTruCturE(C(Na, 21L, nA, 8L, 8l, 8L, 8l),.labEL = c("", 
"aciDObaCteria_Gp3", "acIdObactEria_gP4", "aCTinoBacTeriA", 
"AlphAproteobacterIa", "BAcilLI", "BaCteroIdeteS_incErTae_seDis", 
"BetAprotEoBacteria", "ChloropLast", "deltaprotEobAcTerIa", 
"flavoBActeriA", "GaMmaProteobActeria
"), class = "factor"), 
X2  = structu re(c( 3L,  1L ,1L,1L,1L, 1L, 1L),.L a bel= c("Root", 
"lineage" , "nu ll " ), c l as s = " factor" ) ,X 3  =st ru ctu re ( c( 1L, 3L,  3L, 3L , 3L, 3L,3L) ,. Label = c("R o ot ", "name",  "r ootrank"
),cla ss = " fa cto r "), X 4 =  stru cture( c (2L, 1 L, 1L, 1L ,1 L, 
1L ,  1L),.L a b el  = c ("Bacteria", "nor an k ", "rank"), cl ass ="f a ct o r "),  
X 5 = struct ur e(c(1 L , 3L, 3 L ,3 L ,  3L ,  3L, 3L),.Lab el = c("194 " , "M2MID 06 _Tr i mmed_n oGaps .f a s",  "domain"),  cla ss = "fac tor"), 
X6 = s t ructure (c(NA,  NA , 1 0L,1 0L ,10L ,1 0L, 10 L), . Lab el = c(" ",  "Acid obac t e r i a","Ac tino bacte ria", "Bacter oid etes " , " Cyano bacte ria/ Ch lorop last",  
"Fi rm icutes", "Gemma timo nadetes",  "N it ros pi ra"," Planct omy cet es", 
" Proteob a cte ri a " ,  " Spirochaetes", "Ve rr u c om icrobia" , "unc l as si f ied_Bact er ia" 
),c l ass =  "fa c to r"), X7= stru c tu re (c(NA,2L , 3L,3L , 3 L,
3L,3 L),. Label= c("","Bact e ria", "phylum" ) , class = "fa c to r " ), 
X8= s tructure(c( NA,2 1L,NA,8 L,  8L ,  8L,8L),. La b el = c("", 
"Acidobact er ia_Gp3 ", "A cidobacteria_ Gp4", "Act i n o bacteria ", " Al p haproteobacter ia","Bacilli", "Bactero idete s_incert ae_sedis" , 
"Betapr ote oba cte ria " ,  " Chloroplast", " Delt ap roteoba cte ria", "Fl avo bac ter ia ", "Gamma proteoba ct er ia 
"), class_= "factor"),_
X2 = structure(c(3L, 1L,_1L, 1L,_1L,_1L, 1L),.Label_=_c("Root", 
"lineage", "null"),_class = "factor"),_X3 = structure(c(1L, 
3L,_3L, 3L, 3L,_3L,_3L),.Label = c("Root", "name", "rootrank"
), class = "factor"), X4 = structure(c(2L, 1L, 1L, 1L,_1L,_
1L, 1L),.Label_=_c("Bacteria",_"no rank", "rank"), class =_"factor"), 
X5 = structure(c(1L, 3L,_3L, 3L,_3L, 3L, 3L),.Label = c("194", 
"M2MID06_Trimmed_noGaps.fas", "domain"), class_=_"factor"), 
X6 =_structure(c(NA, NA, 10L, 10L, 10L, 10L, 10L),.Label = c("",_
"Acidobacteria", "Actinobacteria", "Bacteroidetes", "Cyanobacteria/Chloroplast", 
"Firmicutes", "Gemmatimonadetes",_"Nitrospira", "Planctomycetes", 
"Proteobacteria",_"Spirochaetes",_"Verrucomicrobia",_"unclassified_Bacteria"
), class = "factor"),_X7 = structure(c(NA, 2L, 3L, 3L,_3L, 
3L, 3L),.Label = c("", "Bacteria",_"phylum"), class = "factor"), 
X8 = structure(c(NA,_21L, NA, 8L, 8L, 8L, 8L),.Label_= c("", 
"Acidobacteria_Gp3", "Acidobacteria_Gp4", "Actinobacteria",_
"Alphaproteobacteria", "Bacilli",_"Bacteroidetes_incertae_sedis", 
"Betaproteobacteria", "Chloroplast", "Deltaproteobacteria", 
"Flavobacteria",_"Gammaproteobacteria