diff --git a/doc/1_reference_legio_phylo.Rnw b/doc/1_reference_legio_phylo.Rnw
index 9b7a32f7340f1cd73e760239192805dda8f4cf6e..c8907eb193c6c47b68feae50600ec2e89e2f3ad1 100644
--- a/doc/1_reference_legio_phylo.Rnw
+++ b/doc/1_reference_legio_phylo.Rnw
@@ -331,7 +331,7 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p
<<>>=
library(ape)
-aln<-paste0(home, "fasta/78Lp/")
+aln<-paste0(home, "fasta/78Lp_V2/")
subrep<-list.files(aln)
subrep<-subrep[grep(x=subrep, pattern="Q5")]
subrep
@@ -348,8 +348,10 @@ file<-list.files(paste0(aln, "/", subrepcurrent))
file<-file[grep(x=file, pattern="aln")]
if (length(file)>0){
fasta<-read.dna(paste0(aln, "/",subrepcurrent, "/", file), format="fasta", as.character=TRUE)
- rownames(fasta)<-sapply(rownames(fasta), function(x) strsplit(x, split=".", fixed=TRUE)[[1]][1])
- cat<-c(cat, rownames(fasta))
+ tmprownames<-ifelse(grepl(rownames(fasta), pattern = "pneumo"),
+ substr(rownames(fasta)[grep(pattern = "pneumophila",rownames(fasta))], 1,31),
+ sapply(rownames(fasta), function(x) strsplit(x, split=".", fixed=TRUE)[[1]][1]))
+ cat<-c(cat, tmprownames)
}
}
@@ -364,14 +366,17 @@ colnames(tab)<-subrep
# make a cat list containing all species names
for (subrepcurrent in subrep){
-print(subrepcurrent)
+#print(subrepcurrent)
file<-list.files(paste0(aln, "/", subrepcurrent))
file<-file[grep(x=file, pattern="aln")]
if (length(file)>0){
fasta<-read.dna(paste0(aln, "/",subrepcurrent, "/", file), format="fasta", as.character=TRUE)
- rownames(fasta)<-sapply(rownames(fasta), function(x) strsplit(x, split=".", fixed=TRUE)[[1]][1])
- tmp<-ifelse(rownames(tab) %in% rownames(fasta), 1, 0)
+ tmprownames<-ifelse(grepl(rownames(fasta), pattern = "pneumo"),
+ substr(rownames(fasta)[grep(pattern = "pneumophila",rownames(fasta))], 1,31),
+ sapply(rownames(fasta), function(x) strsplit(x, split=".", fixed=TRUE)[[1]][1]))
+
+ tmp<-ifelse(rownames(tab) %in% tmprownames, 1, 0)
tab[,subrepcurrent]<-tmp
}
}
@@ -397,7 +402,7 @@ barplot(vectgene, horiz=TRUE, las=2)
\subsection{Concatenate and Supertree}
<<tree, fig.height=12>>=
-treepath<-paste0(home, "fasta/78Lp/cat.phylip_phyml_tree")
+treepath<-paste0(home, "fasta/78Lp_V2/cat.phylip_phyml_tree")
tree<-read.tree(treepath)
plot(root(tree, outgroup = "Coxiella_burnetii"))
diff --git a/doc/1_reference_legio_phylo.aux b/doc/1_reference_legio_phylo.aux
index 05788fefe4c078076c22c2c073cda4a54447470f..16fa2758ad7b946bc505e87cffafad514759911b 100644
--- a/doc/1_reference_legio_phylo.aux
+++ b/doc/1_reference_legio_phylo.aux
@@ -20,11 +20,11 @@
\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}Objective}{2}{subsection.1.1}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}Data}{2}{subsection.1.2}}
\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.1}Data from the first publication:}{2}{subsubsection.1.2.1}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.2}Data from the seconde publication:}{5}{subsubsection.1.2.2}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.3}Data from Legionella pneumophila reference strains:}{13}{subsubsection.1.2.3}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}Add missing species}{14}{subsection.1.3}}
-\@writefile{toc}{\contentsline {section}{\numberline {2}Get genes sequences}{15}{section.2}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Get sequences from Burstein et al.}{15}{subsection.2.1}}
-\@writefile{toc}{\contentsline {section}{\numberline {3}Phylogeny}{16}{section.3}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Genes alignement}{16}{subsection.3.1}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Concatenate and Supertree}{26}{subsection.3.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.2}Data from the seconde publication:}{4}{subsubsection.1.2.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.3}Data from Legionella pneumophila reference strains:}{10}{subsubsection.1.2.3}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}Add missing species}{11}{subsection.1.3}}
+\@writefile{toc}{\contentsline {section}{\numberline {2}Get genes sequences}{12}{section.2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Get sequences from Burstein et al.}{12}{subsection.2.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {3}Phylogeny}{13}{section.3}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Genes alignement}{13}{subsection.3.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Concatenate and Supertree}{20}{subsection.3.2}}
diff --git a/doc/1_reference_legio_phylo.log b/doc/1_reference_legio_phylo.log
index 078f7758357f42ceaa235044e647bac4849f4dda..78c41e7d2344f44406333f6c021fc2e226591504 100644
--- a/doc/1_reference_legio_phylo.log
+++ b/doc/1_reference_legio_phylo.log
@@ -1,4 +1,4 @@
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entering extended mode
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[][]\OT1/cmtt/m/n/10.95 tab1[][]<-[][]read.table[][]([][]paste0[][](data, datal
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n\OT1/cmtt/m/n/10.95 t"[][],[] []fill[][]=[][]TRUE[][],[] []header[][]=[][]TRUE
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[]
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+ Isolation ORF.prefix[]
+ []
+
+
+Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+[]\OT1/cmtt/m/n/10.95 ## 1 L. adelaidensis ATCC49625 ATCC49625 Wa
+ter in cooling tower (Adelaide, Australia) Lade[]
+ []
+
+
+Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+[]\OT1/cmtt/m/n/10.95 ## 2 L. anisa ATCC35292 WA-316-C3
+ Tap water (Los Angeles, CA, USA) Lani[]
+ []
+
+
+Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+[]\OT1/cmtt/m/n/10.95 ## 3 L. birminghamensis ATCC43702 CDC#1407-AL-14
+ Lung biopsy (Alabama, USA) Lbir[]
+ []
+
+
+Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+[]\OT1/cmtt/m/n/10.95 ## 4 L. bozemanii ATCC33217 WIGA
+ Lung tissue (Key West, FL, USA) Lboz[]
+ []
+
+
+Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+[]\OT1/cmtt/m/n/10.95 ## 5 L. brunensis ATCC43878 ATCC43878
+ Cooling tower water (Czechoslovakia) Lbru[]
+ []
+
+
+Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+[]\OT1/cmtt/m/n/10.95 ## 6 L. cherrii ATCC35252 ORW
+ Thermally altered water (Minnesota, USA) Lche[]
+ []
+
+[2]
+Package xcolor Warning: Incompatible color definition on input line 163.
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+
+Overfull \hbox (392.80441pt too wide) in paragraph at lines 165--165
[][]\OT1/cmtt/m/n/10.95 tabPRJNA[][]<-[][]read.table[][]([][]paste0[][](data,[]
[]"PRJNA285910_AssemblyDetails.txt"[][]),[] []header[][]=[][]FALSE[][],[] []se
p[][]=[][]"\OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/n/10.95 t"[][],[] []skip[][]=[][]2[
@@ -797,27 +887,99 @@ p[][]=[][]"\OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/n/10.95 t"[][],[] []skip[][]=[][]2[
[]
-Overfull \hbox (209.12009pt too wide) in paragraph at lines 183--183
+Overfull \hbox (209.12009pt too wide) in paragraph at lines 168--168
[][]\OT1/cmtt/m/n/10.95 names[][](tabPRJNA)[][]<-[][]c[][]([][]"Assembly"[][],[
] []"Level"[][],[] []"WGS"[][],[] []"BioSample"[][],[] []"Strain"[]
[],[] []"Taxonomy"[][])[][]
[]
-Overfull \hbox (7.91602pt too wide) in paragraph at lines 241--241
-[]\OT1/cmtt/m/n/10.95 ## 38 Levels: Fluoribacter dumoffii NY 23 ... Tatlockia m
-icdadei[]
+Overfull \hbox (209.12009pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## [1] Fluoribacter dumoffii NY 23 Fluoribacter go
+rmanii Legionella adelaidensis[]
+ []
+
+
+Overfull \hbox (191.87402pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## [4] Legionella anisa Legionella birm
+inghamensis Legionella bozemanae[]
+ []
+
+
+Overfull \hbox (226.36615pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## [7] Legionella brunensis Legionella cher
+rii Legionella cincinnatiensis[]
+ []
+
+
+Overfull \hbox (180.37665pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## [10] Legionella drozanskii LLAP-1 Legionella eryt
+hra Legionella feeleii[]
[]
-[3] [4]
-Package xcolor Warning: Incompatible color definition on input line 247.
+Overfull \hbox (191.87402pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## [13] Legionella geestiana Legionella grat
+iana Legionella hackeliae[]
+ []
-Package xcolor Warning: Incompatible color definition on input line 259.
+Overfull \hbox (186.12534pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## [16] Legionella israelensis Legionella jame
+stowniensis Legionella jordanis[]
+ []
-Overfull \hbox (208.8464pt too wide) in paragraph at lines 269--269
+Overfull \hbox (209.12009pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## [19] Legionella lansingensis Legionella lond
+iniensis Legionella maceachernii[]
+ []
+
+
+Overfull \hbox (209.12009pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## [22] Legionella moravica Legionella naut
+arum Legionella oakridgensis[]
+ []
+
+
+Overfull \hbox (203.3714pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## [25] Legionella parisiensis Legionella quat
+eirensis Legionella quinlivanii[]
+ []
+
+
+Overfull \hbox (203.3714pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## [28] Legionella rubrilucens Legionella sain
+thelensi Legionella santicrucis[]
+ []
+
+
+Overfull \hbox (180.37665pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## [31] Legionella shakespearei DSM 23087 Legionella spir
+itensis Legionella steelei[]
+ []
+
+
+Overfull \hbox (191.87402pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## [34] Legionella steigerwaltii Legionella tucs
+onensis Legionella waltersii[]
+ []
+
+
+Overfull \hbox (272.35565pt too wide) in paragraph at lines 201--201
+[]\OT1/cmtt/m/n/10.95 ## 38 Levels: Fluoribacter dumoffii NY 23 Fluoribacter go
+rmanii Legionella adelaidensis ... Tatlockia micdadei[]
+ []
+
+[3]
+
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+
+
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+
+
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[][]\OT1/cmtt/m/n/10.95 gupta1[][]<-[][]read.table[][]([][]paste0[][](data, dat
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[]
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-[]\OT1/cmtt/m/n/10.95 ##
- Type.Strain[]
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+[]\OT1/cmtt/m/n/10.95 ## Species
+ Type.Strain[]
[]
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-[]\OT1/cmtt/m/n/10.95 ## 1 1762-Aus-E; ATCC 49625; CCUG 31231 A; CIP 1
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+[]\OT1/cmtt/m/n/10.95 ## 1 Legionella adelaidensis 1762-Aus-E; ATCC
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[]
-Overfull \hbox (128.63846pt too wide) in paragraph at lines 302--302
-[]\OT1/cmtt/m/n/10.95 ## 2 ATCC 35292; CCUG 29665; CIP 103870; DSM 17627; JCM
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+[]\OT1/cmtt/m/n/10.95 ## 2 Legionella anisa ATCC 35292; CCUG 29665;
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[]
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-9liard A1; Montb\xe9liard A1[]
+Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255
+[]\OT1/cmtt/m/n/10.95 ## 3 Legionella beliardensis ATCC 700512; CIP
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[]
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-[]\OT1/cmtt/m/n/10.95 ## 4 1407-AL-H; ATCC 43702; CCUG 31233 A; CIP 103871; DSM
- 19232; JCM 7559; NCTC 12437[]
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+[]\OT1/cmtt/m/n/10.95 ## 4 Legionella birminghamensis 1407-AL-H; ATCC 43702; CC
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[]
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-[]\OT1/cmtt/m/n/10.95 ## 5 ALLO1; ATCC 33217;
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+[]\OT1/cmtt/m/n/10.95 ## 5 Legionella bozemanae
+ ALLO1; ATCC 33217; CIP 103872; DSM 16523; WIGA[]
[]
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-[]\OT1/cmtt/m/n/10.95 ## 6 441-1; ATCC 43878; CCUG 31114; CIP 1
-03874; DSM 19236; NCTC 12240[]
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+[]\OT1/cmtt/m/n/10.95 ## 6 Legionella brunensis 441-1; AT
+CC 43878; CCUG 31114; CIP 103874; DSM 19236; NCTC 12240[]
[]
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f_Assemblies[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 1 1762-Aus-E Y
3[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 2 <NA> N
5[]
[]
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2[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 4 1407-AL-H Y
3[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 5 WIGA Y
5[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 6 ATCC 43878 Y
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[]
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[][]\OT1/cmtt/m/it/10.95 #gupta2<-read.table(paste0(data, datalist2[2]), sep="\
OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/it/10.95 t", fill=TRUE, header=TRUE, comment.ch
ar = "")[][]
[]
-[5]
+[4]
-Package xcolor Warning: Incompatible color definition on input line 314.
+Package xcolor Warning: Incompatible color definition on input line 267.
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-[]\OT1/cmtt/m/n/10.95 ## 38 Levels: Fluoribacter dumoffii NY 23 ... Tatlockia m
-icdadei[]
+Overfull \hbox (226.36615pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## [1] Legionella adelaidensis Legionella anis
+a Legionella birminghamensis[]
[]
-Overfull \hbox (7.91602pt too wide) in paragraph at lines 444--444
-[]\OT1/cmtt/m/n/10.95 ## 38 Levels: Fluoribacter dumoffii NY 23 ... Tatlockia m
-icdadei[]
+Overfull \hbox (180.37665pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## [4] Legionella bozemanae Legionella brun
+ensis Legionella cherrii[]
[]
-[6] [7] [8]
-Package xcolor Warning: Incompatible color definition on input line 456.
+Overfull \hbox (180.37665pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## [7] Legionella cincinnatiensis Legionella droz
+anskii LLAP-1 Legionella erythra[]
+ []
+
+Overfull \hbox (186.12534pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## [10] Legionella feeleii Legionella gees
+tiana Legionella gratiana[]
+ []
-Overfull \hbox (140.13583pt too wide) in paragraph at lines 459--459
+
+Overfull \hbox (226.36615pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## [13] Legionella hackeliae Legionella isra
+elensis Legionella jamestowniensis[]
+ []
+
+
+Overfull \hbox (209.12009pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## [16] Legionella jordanis Legionella lans
+ingensis Legionella londiniensis[]
+ []
+
+
+Overfull \hbox (186.12534pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## [19] Legionella maceachernii Legionella mora
+vica Legionella nautarum[]
+ []
+
+
+Overfull \hbox (209.12009pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## [22] Legionella oakridgensis Legionella pari
+siensis Legionella quateirensis[]
+ []
+
+
+Overfull \hbox (209.12009pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## [25] Legionella quinlivanii Legionella rubr
+ilucens Legionella sainthelensi[]
+ []
+
+
+Overfull \hbox (203.3714pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## [28] Legionella santicrucis Legionella shak
+espearei DSM 23087 Legionella spiritensis[]
+ []
+
+
+Overfull \hbox (203.3714pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## [31] Legionella steelei Legionella stei
+gerwaltii Legionella tucsonensis[]
+ []
+
+
+Overfull \hbox (13.6647pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## [34] Legionella waltersii Legionella wors
+leiensis[]
+ []
+
+
+Overfull \hbox (272.35565pt too wide) in paragraph at lines 288--288
+[]\OT1/cmtt/m/n/10.95 ## 38 Levels: Fluoribacter dumoffii NY 23 Fluoribacter go
+rmanii Legionella adelaidensis ... Tatlockia micdadei[]
+ []
+
+
+Overfull \hbox (266.60696pt too wide) in paragraph at lines 310--310
+[]\OT1/cmtt/m/n/10.95 ## [1] Legionella adelaidensis Legionella anisa
+ Legionella birminghamensis Legionella bozemanae[]
+ []
+
+
+Overfull \hbox (255.10959pt too wide) in paragraph at lines 310--310
+[]\OT1/cmtt/m/n/10.95 ## [5] Legionella brunensis Legionella cherrii
+ Legionella cincinnatiensis Legionella erythra[]
+ []
+
+
+Overfull \hbox (266.60696pt too wide) in paragraph at lines 310--310
+[]\OT1/cmtt/m/n/10.95 ## [9] Legionella feeleii Legionella geestiana
+ Legionella gratiana Legionella hackeliae[]
+ []
+
+
+Overfull \hbox (283.85303pt too wide) in paragraph at lines 310--310
+[]\OT1/cmtt/m/n/10.95 ## [13] Legionella israelensis Legionella jamestownie
+nsis Legionella jordanis Legionella lansingensis[]
+ []
+
+
+Overfull \hbox (260.85828pt too wide) in paragraph at lines 310--310
+[]\OT1/cmtt/m/n/10.95 ## [17] Legionella londiniensis Legionella maceacherni
+i Legionella moravica Legionella nautarum[]
+ []
+
+
+Overfull \hbox (278.10434pt too wide) in paragraph at lines 310--310
+[]\OT1/cmtt/m/n/10.95 ## [21] Legionella oakridgensis Legionella parisiensis
+ Legionella quateirensis Legionella quinlivanii[]
+ []
+
+
+Overfull \hbox (278.10434pt too wide) in paragraph at lines 310--310
+[]\OT1/cmtt/m/n/10.95 ## [25] Legionella rubrilucens Legionella sainthelens
+i Legionella santicrucis Legionella spiritensis[]
+ []
+
+
+Overfull \hbox (266.60696pt too wide) in paragraph at lines 310--310
+[]\OT1/cmtt/m/n/10.95 ## [29] Legionella steelei Legionella steigerwalt
+ii Legionella tucsonensis Legionella waltersii[]
+ []
+
+
+Overfull \hbox (197.62271pt too wide) in paragraph at lines 310--310
+[]\OT1/cmtt/m/n/10.95 ## 73 Levels: Aquicella lusitana Aquicella siphonis Burkh
+olderia cepacia ... Rickettsiella grylli[]
+ []
+
+
+Overfull \hbox (99.89502pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [1] Legionella beliardensis
+Legionella clemsonensis[]
+ []
+
+
+Overfull \hbox (88.39764pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [3] Legionella drancourtii
+Legionella drozanskii[]
+ []
+
+
+Overfull \hbox (243.61221pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [5] Legionella dumoffii NY23
+Legionella endosymbiont of Polyplax serrata PsAG[]
+ []
+
+
+Overfull \hbox (76.90027pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [7] Legionella fairfieldensis
+Legionella fallonii[]
+ []
+
+
+Overfull \hbox (94.14633pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [9] Legionella gormanii
+Legionella impletisoli[]
+ []
+
+
+Overfull \hbox (99.89502pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [11] Legionella longbeachae
+Legionella massiliensis[]
+ []
+
+
+Overfull \hbox (105.6437pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [13] Legionella micdadei
+Legionella nagasakiensis[]
+ []
+
+
+Overfull \hbox (94.14633pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [15] Legionella norrlandica
+Legionella pneumophila[]
+ []
+
+
+Overfull \hbox (94.14633pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [17] Legionella rowbothamii
+Legionella saoudiensis[]
+ []
+
+
+Overfull \hbox (94.14633pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [19] Legionella shakespearei
+Legionella taurinensis[]
+ []
+
+
+Overfull \hbox (94.14633pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [21] Legionella tunisiensis
+Legionella wadsworthii[]
+ []
+
+
+Overfull \hbox (134.38715pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [23] Legionella yabuuchiae
+Candidatus Coxiella mudrowiae[]
+ []
+
+
+Overfull \hbox (226.36615pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [25] Coxiella burnetii
+Coxiella endosymbiont of Amblyomma americanum[]
+ []
+
+
+Overfull \hbox (243.61221pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [27] Coxiella endosymbiont of Amblyomma sculptum
+Coxiella endosymbiont of Rhipicephalus microplus[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [29] Coxiella sp. RIFCSPHIGHO2_12_FULL_42_15
+Coxiella sp. DG_40[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [31] Aquicella lusitana
+Aquicella siphonis[]
+ []
+
+
+Overfull \hbox (168.87927pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [33] Diplorickettsia massiliensis
+Candidatus Rickettsiella isopodorum[]
+ []
+
+
+Overfull \hbox (82.64896pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [35] Candidatus Rickettsiella viridis
+Rickettsiella grylli[]
+ []
+
+
+Overfull \hbox (168.87927pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [37] Candidatus Berkiella aquae
+Candidatus Berkiella cookevillensis[]
+ []
+
+
+Overfull \hbox (82.64896pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## [39] Burkholderia mallei
+Burkholderia cepacia[]
+ []
+
+
+Overfull \hbox (197.62271pt too wide) in paragraph at lines 337--337
+[]\OT1/cmtt/m/n/10.95 ## 73 Levels: Aquicella lusitana Aquicella siphonis Burkh
+olderia cepacia ... Rickettsiella grylli[]
+ []
+
+
+Overfull \hbox (65.4029pt too wide) in paragraph at lines 345--345
+[]\OT1/cmtt/m/n/10.95 ## [1] Legionella drozanskii LLAP-1 Legionella shake
+spearei DSM 23087[]
+ []
+
+
+Overfull \hbox (272.35565pt too wide) in paragraph at lines 345--345
+[]\OT1/cmtt/m/n/10.95 ## 38 Levels: Fluoribacter dumoffii NY 23 Fluoribacter go
+rmanii Legionella adelaidensis ... Tatlockia micdadei[]
+ []
+
+[5] [6]
+
+Package xcolor Warning: Incompatible color definition on input line 357.
+
+
+Overfull \hbox (140.13583pt too wide) in paragraph at lines 360--360
[][]\OT1/cmtt/m/n/10.95 guptasp[][]<-[][]guptasp[guptasp[] []%in%[] []c[][]([][
]"Legionella drozanskii"[][],[] []"Legionella shakespearei"[][])[][]==[][]F][][
]
[]
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+Overfull \hbox (99.89502pt too wide) in paragraph at lines 377--377
+[]\OT1/cmtt/m/n/10.95 ## [1] Legionella beliardensis
+Legionella clemsonensis[]
+ []
+
+
+Overfull \hbox (105.6437pt too wide) in paragraph at lines 377--377
+[]\OT1/cmtt/m/n/10.95 ## [3] Legionella drancourtii
+Legionella dumoffii NY23[]
+ []
+
+
+Overfull \hbox (111.3924pt too wide) in paragraph at lines 377--377
+[]\OT1/cmtt/m/n/10.95 ## [5] Legionella endosymbiont of Polyplax serrata PsAG
+Legionella fairfieldensis[]
+ []
+
+
+Overfull \hbox (76.90027pt too wide) in paragraph at lines 377--377
+[]\OT1/cmtt/m/n/10.95 ## [7] Legionella fallonii
+Legionella gormanii[]
+ []
+
+
+Overfull \hbox (94.14633pt too wide) in paragraph at lines 377--377
+[]\OT1/cmtt/m/n/10.95 ## [9] Legionella impletisoli
+Legionella longbeachae[]
+ []
+
+
+Overfull \hbox (76.90027pt too wide) in paragraph at lines 377--377
+[]\OT1/cmtt/m/n/10.95 ## [11] Legionella massiliensis
+Legionella micdadei[]
+ []
+
+
+Overfull \hbox (94.14633pt too wide) in paragraph at lines 377--377
+[]\OT1/cmtt/m/n/10.95 ## [13] Legionella nagasakiensis
+Legionella norrlandica[]
+ []
+
+
+Overfull \hbox (94.14633pt too wide) in paragraph at lines 377--377
+[]\OT1/cmtt/m/n/10.95 ## [15] Legionella pneumophila
+Legionella rowbothamii[]
+ []
+
+
+Overfull \hbox (94.14633pt too wide) in paragraph at lines 377--377
+[]\OT1/cmtt/m/n/10.95 ## [17] Legionella saoudiensis
+Legionella taurinensis[]
+ []
+
+
+Overfull \hbox (94.14633pt too wide) in paragraph at lines 377--377
+[]\OT1/cmtt/m/n/10.95 ## [19] Legionella tunisiensis
+Legionella wadsworthii[]
+ []
+
+
+Overfull \hbox (197.62271pt too wide) in paragraph at lines 377--377
+[]\OT1/cmtt/m/n/10.95 ## 73 Levels: Aquicella lusitana Aquicella siphonis Burkh
+olderia cepacia ... Rickettsiella grylli[]
+ []
+
+
+Overfull \hbox (42.40814pt too wide) in paragraph at lines 380--380
[][]\OT1/cmtt/m/n/10.95 guptasp[][]<-[][]c[][]([][]as.character[][](guptasp[[][
]grep[][](guptasp,[] []pattern[][]=[][]"Legionella"[][])]),[][]
[]
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+Overfull \hbox (42.40814pt too wide) in paragraph at lines 381--381
[] []\OT1/cmtt/m/n/10.95 as.character[][](guptasp[[][]grep[][](guptasp,[] []
pattern[][]=[][]"Coxiella burnetii"[][])]))[][]
[]
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+Overfull \hbox (277.54225pt too wide) in paragraph at lines 387--387
[][]\OT1/cmtt/m/it/10.95 ## remove \OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/it/10.95 te
xtit\OMS/cmsy/m/n/10.95 f\OT1/cmtt/m/it/10.95 Fluoribacter dumoffii\OMS/cmsy/m/
n/10.95 g \OT1/cmtt/m/it/10.95 NY 23, \OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/it/10.95
@@ -1009,389 +1495,495 @@ n/10.95 g \OT1/cmtt/m/it/10.95 NY 23, \OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/it/10.95
n/10.95 g\OT1/cmtt/m/it/10.95 .[][]
[]
-[9]
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+Package xcolor Warning: Incompatible color definition on input line 400.
+
+[7]
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+[]\OT1/cmtt/m/n/10.95 ## Species Nu
+mber_of_Assemblies[]
+ []
+
+
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+[]\OT1/cmtt/m/n/10.95 ## 3 Legionella beliardensis
+ 2[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 9 Legionella clemsonensis
+ 1[]
+ []
+
+
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+[]\OT1/cmtt/m/n/10.95 ## 10 Legionella drancourtii
+ 1[]
+ []
+
+
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+[]\OT1/cmtt/m/n/10.95 ## 13 Legionella endosymbiont of Polyplax serrata PsAG
+ 1[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 15 Legionella fairfieldensis
+ 2[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 16 Legionella fallonii
+ 1[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 22 Legionella impletisoli
+ 1[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 28 Legionella longbeachae
+ 9[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 30 Legionella massiliensis
+ 2[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 33 Legionella nagasakiensis
+ 1[]
+ []
+
+
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+[]\OT1/cmtt/m/n/10.95 ## 35 Legionella norrlandica
+ 1[]
+ []
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 41 Legionella rowbothamii
+ 1[]
+ []
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+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 45 Legionella saoudiensis
+ 1[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 50 Legionella taurinensis
+ 16[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 52 Legionella tunisiensis
+ 1[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 53 Legionella wadsworthii
+ 3[]
+ []
+
+
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+[]\OT1/cmtt/m/n/10.95 ## 56 Legionella yabuuchiae
+ 1[]
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 58 Coxiella burnetii
+ 69[]
+ []
+
+
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[]\OT1/cmtt/m/n/10.95 ## Available_Genome_Accession_Number_.Ref_Seq_is_provi
ded_when_available.[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 3
NZ_UGNV01000001.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 9
NZ_CP016397.1[]
[]
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NZ_JH413847.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 13
NZ_CP021497.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 15
NZ_JHYC01000001.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 16
NZ_LN614827.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 22 N
Z_CAAAIA010000001.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 28
NC_013861.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 30
NZ_CCVW01000001.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 33 N
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[]
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[]\OT1/cmtt/m/n/10.95 ## 35
NZ_JNCF01000001.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 41 N
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[]
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[]\OT1/cmtt/m/n/10.95 ## 45
NZ_LN901324.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 50
NZ_QCXN01000001.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 52
NZ_CALJ01000248.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 53
NZ_KL370759.1[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 56 N
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NZ_CP013667.1[]
[]
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[]
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[]
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[]
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[]
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[]
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[]
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[]
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[][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][
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[][]\OT1/cmtt/m/n/10.95 tabAsstmp[][]<-[][]cbind[][](guptaonly[][]$[][]Assembly
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[][]\OT1/cmtt/m/n/10.95 ncbi[][]<-[][]read.table[][]([][]paste0[][](data,[] []"
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[]\OT1/cmr/m/n/10.95 Legionella pneu-mophila Paris com-plete genome : CR628336.
1 - GCA[]000048645.1
[]
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[]\OT1/cmr/m/n/10.95 Legionella pneu-mophila Lens com-plete genome : CR628337.1
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[]\OT1/cmr/m/n/10.95 Legionella pneu-mophila Corby com-plete genome : NC[]00949
4 - GCA[]000092545.1
[]
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[]\OT1/cmr/m/n/10.95 Legionella pneu-mophila Al-coy com-plete genome : NC[]0141
25 - GCA[]000092625.1
[]
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[]\OT1/cmr/m/n/10.95 Optionnel : Le-gionella pneu-mophila Lor-raine com-plete g
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[][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss,[] []c[][]([][]"GCA
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[][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss_V2,[] []c[][]([][]"
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[][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss_V2,[] []c[][]([][]"
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[][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss_V2,[] []c[][]([][]"
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diff --git a/doc/1_reference_legio_phylo.pdf b/doc/1_reference_legio_phylo.pdf
index b537326dc4235616d80a5e27bbd0955b2e4ce10c..e7ccefddc522613c2affb660c2fcefff61386c6e 100644
Binary files a/doc/1_reference_legio_phylo.pdf and b/doc/1_reference_legio_phylo.pdf differ
diff --git a/doc/1_reference_legio_phylo.tex b/doc/1_reference_legio_phylo.tex
index f06946c0d3db0b08792c4bae4213a2650f52a317..047c198051da11d6d5f76877d188d53834dd3f65 100644
--- a/doc/1_reference_legio_phylo.tex
+++ b/doc/1_reference_legio_phylo.tex
@@ -122,22 +122,14 @@ We chose to use the 78 genes selected by Burstein et al. 2016. The first objecti
\hlstd{datalist1}
\end{alltt}
\begin{verbatim}
-## [1] "NIHMS817051-supplement-Supplemental_Table_1.csv"
-## [2] "NIHMS817051-supplement-Supplemental_Table_1.xlsx"
-## [3] "NIHMS817051-supplement-Supplemental_Table_10.csv"
-## [4] "NIHMS817051-supplement-Supplemental_Table_10.xlsx"
-## [5] "NIHMS817051-supplement-Supplemental_Table_11.xlsx"
-## [6] "NIHMS817051-supplement-Supplemental_Table_12.xlsx"
-## [7] "NIHMS817051-supplement-Supplemental_Table_2.xlsx"
-## [8] "NIHMS817051-supplement-Supplemental_Table_3_tmp.xlsx"
-## [9] "NIHMS817051-supplement-Supplemental_Table_3.csv"
-## [10] "NIHMS817051-supplement-Supplemental_Table_3.xlsx"
-## [11] "NIHMS817051-supplement-Supplemental_Table_4.xlsx"
-## [12] "NIHMS817051-supplement-Supplemental_Table_5.xlsx"
-## [13] "NIHMS817051-supplement-Supplemental_Table_6.xlsx"
-## [14] "NIHMS817051-supplement-Supplemental_Table_7.xlsx"
-## [15] "NIHMS817051-supplement-Supplemental_Table_8.xlsx"
-## [16] "NIHMS817051-supplement-Supplemental_Table_9.xlsx"
+## [1] "NIHMS817051-supplement-Supplemental_Table_1.csv" "NIHMS817051-supplement-Supplemental_Table_1.xlsx"
+## [3] "NIHMS817051-supplement-Supplemental_Table_10.csv" "NIHMS817051-supplement-Supplemental_Table_10.xlsx"
+## [5] "NIHMS817051-supplement-Supplemental_Table_11.xlsx" "NIHMS817051-supplement-Supplemental_Table_12.xlsx"
+## [7] "NIHMS817051-supplement-Supplemental_Table_2.xlsx" "NIHMS817051-supplement-Supplemental_Table_3_tmp.xlsx"
+## [9] "NIHMS817051-supplement-Supplemental_Table_3.csv" "NIHMS817051-supplement-Supplemental_Table_3.xlsx"
+## [11] "NIHMS817051-supplement-Supplemental_Table_4.xlsx" "NIHMS817051-supplement-Supplemental_Table_5.xlsx"
+## [13] "NIHMS817051-supplement-Supplemental_Table_6.xlsx" "NIHMS817051-supplement-Supplemental_Table_7.xlsx"
+## [15] "NIHMS817051-supplement-Supplemental_Table_8.xlsx" "NIHMS817051-supplement-Supplemental_Table_9.xlsx"
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -149,20 +141,13 @@ We chose to use the 78 genes selected by Burstein et al. 2016. The first objecti
\hlkwd{head}\hlstd{(tab1)}
\end{alltt}
\begin{verbatim}
-## Species ATCC.number Strain.designation
-## 1 L. adelaidensis ATCC49625 ATCC49625
-## 2 L. anisa ATCC35292 WA-316-C3
-## 3 L. birminghamensis ATCC43702 CDC#1407-AL-14
-## 4 L. bozemanii ATCC33217 WIGA
-## 5 L. brunensis ATCC43878 ATCC43878
-## 6 L. cherrii ATCC35252 ORW
-## Isolation ORF.prefix
-## 1 Water in cooling tower (Adelaide, Australia) Lade
-## 2 Tap water (Los Angeles, CA, USA) Lani
-## 3 Lung biopsy (Alabama, USA) Lbir
-## 4 Lung tissue (Key West, FL, USA) Lboz
-## 5 Cooling tower water (Czechoslovakia) Lbru
-## 6 Thermally altered water (Minnesota, USA) Lche
+## Species ATCC.number Strain.designation Isolation ORF.prefix
+## 1 L. adelaidensis ATCC49625 ATCC49625 Water in cooling tower (Adelaide, Australia) Lade
+## 2 L. anisa ATCC35292 WA-316-C3 Tap water (Los Angeles, CA, USA) Lani
+## 3 L. birminghamensis ATCC43702 CDC#1407-AL-14 Lung biopsy (Alabama, USA) Lbir
+## 4 L. bozemanii ATCC33217 WIGA Lung tissue (Key West, FL, USA) Lboz
+## 5 L. brunensis ATCC43878 ATCC43878 Cooling tower water (Czechoslovakia) Lbru
+## 6 L. cherrii ATCC35252 ORW Thermally altered water (Minnesota, USA) Lche
## Accession Version BioSample BioProject
## 1 LNKA00000000 LNKA01000000 SAMN03842654 PRJNA285910
## 2 LNXS00000000 LNXS01000000 SAMN04274764 PRJNA285910
@@ -199,45 +184,20 @@ We chose to use the 78 genes selected by Burstein et al. 2016. The first objecti
\hlstd{tabAss}\hlopt{$}\hlstd{Taxonomy}
\end{alltt}
\begin{verbatim}
-## [1] Fluoribacter dumoffii NY 23
-## [2] Fluoribacter gormanii
-## [3] Legionella adelaidensis
-## [4] Legionella anisa
-## [5] Legionella birminghamensis
-## [6] Legionella bozemanae
-## [7] Legionella brunensis
-## [8] Legionella cherrii
-## [9] Legionella cincinnatiensis
-## [10] Legionella drozanskii LLAP-1
-## [11] Legionella erythra
-## [12] Legionella feeleii
-## [13] Legionella geestiana
-## [14] Legionella gratiana
-## [15] Legionella hackeliae
-## [16] Legionella israelensis
-## [17] Legionella jamestowniensis
-## [18] Legionella jordanis
-## [19] Legionella lansingensis
-## [20] Legionella londiniensis
-## [21] Legionella maceachernii
-## [22] Legionella moravica
-## [23] Legionella nautarum
-## [24] Legionella oakridgensis
-## [25] Legionella parisiensis
-## [26] Legionella quateirensis
-## [27] Legionella quinlivanii
-## [28] Legionella rubrilucens
-## [29] Legionella sainthelensi
-## [30] Legionella santicrucis
-## [31] Legionella shakespearei DSM 23087
-## [32] Legionella spiritensis
-## [33] Legionella steelei
-## [34] Legionella steigerwaltii
-## [35] Legionella tucsonensis
-## [36] Legionella waltersii
-## [37] Legionella worsleiensis
-## [38] Tatlockia micdadei
-## 38 Levels: Fluoribacter dumoffii NY 23 ... Tatlockia micdadei
+## [1] Fluoribacter dumoffii NY 23 Fluoribacter gormanii Legionella adelaidensis
+## [4] Legionella anisa Legionella birminghamensis Legionella bozemanae
+## [7] Legionella brunensis Legionella cherrii Legionella cincinnatiensis
+## [10] Legionella drozanskii LLAP-1 Legionella erythra Legionella feeleii
+## [13] Legionella geestiana Legionella gratiana Legionella hackeliae
+## [16] Legionella israelensis Legionella jamestowniensis Legionella jordanis
+## [19] Legionella lansingensis Legionella londiniensis Legionella maceachernii
+## [22] Legionella moravica Legionella nautarum Legionella oakridgensis
+## [25] Legionella parisiensis Legionella quateirensis Legionella quinlivanii
+## [28] Legionella rubrilucens Legionella sainthelensi Legionella santicrucis
+## [31] Legionella shakespearei DSM 23087 Legionella spiritensis Legionella steelei
+## [34] Legionella steigerwaltii Legionella tucsonensis Legionella waltersii
+## [37] Legionella worsleiensis Tatlockia micdadei
+## 38 Levels: Fluoribacter dumoffii NY 23 Fluoribacter gormanii Legionella adelaidensis ... Tatlockia micdadei
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -271,20 +231,13 @@ We keep only legionella, not \textit{Fluoribacter dumoffii} NY 23, \textit{Fluor
\hlkwd{head}\hlstd{(gupta1)}
\end{alltt}
\begin{verbatim}
-## Species
-## 1 Legionella adelaidensis
-## 2 Legionella anisa
-## 3 Legionella beliardensis
-## 4 Legionella birminghamensis
-## 5 Legionella bozemanae
-## 6 Legionella brunensis
-## Type.Strain
-## 1 1762-Aus-E; ATCC 49625; CCUG 31231 A; CIP 103645; DSM 19888; NCTC 12735
-## 2 ATCC 35292; CCUG 29665; CIP 103870; DSM 17627; JCM 7573; NCTC 11974; WA-316-C3
-## 3 ATCC 700512; CIP 106632; DSM 19152; Montb\xe9liard A1; Montb\xe9liard A1
-## 4 1407-AL-H; ATCC 43702; CCUG 31233 A; CIP 103871; DSM 19232; JCM 7559; NCTC 12437
-## 5 ALLO1; ATCC 33217; CIP 103872; DSM 16523; WIGA
-## 6 441-1; ATCC 43878; CCUG 31114; CIP 103874; DSM 19236; NCTC 12240
+## Species Type.Strain
+## 1 Legionella adelaidensis 1762-Aus-E; ATCC 49625; CCUG 31231 A; CIP 103645; DSM 19888; NCTC 12735
+## 2 Legionella anisa ATCC 35292; CCUG 29665; CIP 103870; DSM 17627; JCM 7573; NCTC 11974; WA-316-C3
+## 3 Legionella beliardensis ATCC 700512; CIP 106632; DSM 19152; Montb\xe9liard A1; Montb\xe9liard A1
+## 4 Legionella birminghamensis 1407-AL-H; ATCC 43702; CCUG 31233 A; CIP 103871; DSM 19232; JCM 7559; NCTC 12437
+## 5 Legionella bozemanae ALLO1; ATCC 33217; CIP 103872; DSM 16523; WIGA
+## 6 Legionella brunensis 441-1; ATCC 43878; CCUG 31114; CIP 103874; DSM 19236; NCTC 12240
## Type.Strain.chosen Type_Strain_Availability Number_of_Assemblies
## 1 1762-Aus-E Y 3
## 2 <NA> N 5
@@ -319,42 +272,19 @@ Which species are present in gupta not in the previous datasets.
\hlstd{species}
\end{alltt}
\begin{verbatim}
-## [1] Legionella adelaidensis
-## [2] Legionella anisa
-## [3] Legionella birminghamensis
-## [4] Legionella bozemanae
-## [5] Legionella brunensis
-## [6] Legionella cherrii
-## [7] Legionella cincinnatiensis
-## [8] Legionella drozanskii LLAP-1
-## [9] Legionella erythra
-## [10] Legionella feeleii
-## [11] Legionella geestiana
-## [12] Legionella gratiana
-## [13] Legionella hackeliae
-## [14] Legionella israelensis
-## [15] Legionella jamestowniensis
-## [16] Legionella jordanis
-## [17] Legionella lansingensis
-## [18] Legionella londiniensis
-## [19] Legionella maceachernii
-## [20] Legionella moravica
-## [21] Legionella nautarum
-## [22] Legionella oakridgensis
-## [23] Legionella parisiensis
-## [24] Legionella quateirensis
-## [25] Legionella quinlivanii
-## [26] Legionella rubrilucens
-## [27] Legionella sainthelensi
-## [28] Legionella santicrucis
-## [29] Legionella shakespearei DSM 23087
-## [30] Legionella spiritensis
-## [31] Legionella steelei
-## [32] Legionella steigerwaltii
-## [33] Legionella tucsonensis
-## [34] Legionella waltersii
-## [35] Legionella worsleiensis
-## 38 Levels: Fluoribacter dumoffii NY 23 ... Tatlockia micdadei
+## [1] Legionella adelaidensis Legionella anisa Legionella birminghamensis
+## [4] Legionella bozemanae Legionella brunensis Legionella cherrii
+## [7] Legionella cincinnatiensis Legionella drozanskii LLAP-1 Legionella erythra
+## [10] Legionella feeleii Legionella geestiana Legionella gratiana
+## [13] Legionella hackeliae Legionella israelensis Legionella jamestowniensis
+## [16] Legionella jordanis Legionella lansingensis Legionella londiniensis
+## [19] Legionella maceachernii Legionella moravica Legionella nautarum
+## [22] Legionella oakridgensis Legionella parisiensis Legionella quateirensis
+## [25] Legionella quinlivanii Legionella rubrilucens Legionella sainthelensi
+## [28] Legionella santicrucis Legionella shakespearei DSM 23087 Legionella spiritensis
+## [31] Legionella steelei Legionella steigerwaltii Legionella tucsonensis
+## [34] Legionella waltersii Legionella worsleiensis
+## 38 Levels: Fluoribacter dumoffii NY 23 Fluoribacter gormanii Legionella adelaidensis ... Tatlockia micdadei
\end{verbatim}
\begin{alltt}
\hlkwd{length}\hlstd{(species)}
@@ -367,80 +297,51 @@ Which species are present in gupta not in the previous datasets.
\hlstd{gupta1}\hlopt{$}\hlstd{Species[gupta1}\hlopt{$}\hlstd{Species} \hlopt{%in%} \hlstd{species]}
\end{alltt}
\begin{verbatim}
-## [1] Legionella adelaidensis Legionella anisa
-## [3] Legionella birminghamensis Legionella bozemanae
-## [5] Legionella brunensis Legionella cherrii
-## [7] Legionella cincinnatiensis Legionella erythra
-## [9] Legionella feeleii Legionella geestiana
-## [11] Legionella gratiana Legionella hackeliae
-## [13] Legionella israelensis Legionella jamestowniensis
-## [15] Legionella jordanis Legionella lansingensis
-## [17] Legionella londiniensis Legionella maceachernii
-## [19] Legionella moravica Legionella nautarum
-## [21] Legionella oakridgensis Legionella parisiensis
-## [23] Legionella quateirensis Legionella quinlivanii
-## [25] Legionella rubrilucens Legionella sainthelensi
-## [27] Legionella santicrucis Legionella spiritensis
-## [29] Legionella steelei Legionella steigerwaltii
-## [31] Legionella tucsonensis Legionella waltersii
+## [1] Legionella adelaidensis Legionella anisa Legionella birminghamensis Legionella bozemanae
+## [5] Legionella brunensis Legionella cherrii Legionella cincinnatiensis Legionella erythra
+## [9] Legionella feeleii Legionella geestiana Legionella gratiana Legionella hackeliae
+## [13] Legionella israelensis Legionella jamestowniensis Legionella jordanis Legionella lansingensis
+## [17] Legionella londiniensis Legionella maceachernii Legionella moravica Legionella nautarum
+## [21] Legionella oakridgensis Legionella parisiensis Legionella quateirensis Legionella quinlivanii
+## [25] Legionella rubrilucens Legionella sainthelensi Legionella santicrucis Legionella spiritensis
+## [29] Legionella steelei Legionella steigerwaltii Legionella tucsonensis Legionella waltersii
## [33] Legionella worsleiensis
-## 73 Levels: Aquicella lusitana ... Rickettsiella grylli
+## 73 Levels: Aquicella lusitana Aquicella siphonis Burkholderia cepacia ... Rickettsiella grylli
\end{verbatim}
\begin{alltt}
\hlcom{# Only in Gupta}
\hlstd{gupta1}\hlopt{$}\hlstd{Species[(gupta1}\hlopt{$}\hlstd{Species} \hlopt{%in%} \hlstd{species)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
\end{alltt}
\begin{verbatim}
-## [1] Legionella beliardensis
-## [2] Legionella clemsonensis
-## [3] Legionella drancourtii
-## [4] Legionella drozanskii
-## [5] Legionella dumoffii NY23
-## [6] Legionella endosymbiont of Polyplax serrata PsAG
-## [7] Legionella fairfieldensis
-## [8] Legionella fallonii
-## [9] Legionella gormanii
-## [10] Legionella impletisoli
-## [11] Legionella longbeachae
-## [12] Legionella massiliensis
-## [13] Legionella micdadei
-## [14] Legionella nagasakiensis
-## [15] Legionella norrlandica
-## [16] Legionella pneumophila
-## [17] Legionella rowbothamii
-## [18] Legionella saoudiensis
-## [19] Legionella shakespearei
-## [20] Legionella taurinensis
-## [21] Legionella tunisiensis
-## [22] Legionella wadsworthii
-## [23] Legionella yabuuchiae
-## [24] Candidatus Coxiella mudrowiae
-## [25] Coxiella burnetii
-## [26] Coxiella endosymbiont of Amblyomma americanum
-## [27] Coxiella endosymbiont of Amblyomma sculptum
-## [28] Coxiella endosymbiont of Rhipicephalus microplus
-## [29] Coxiella sp. RIFCSPHIGHO2_12_FULL_42_15
-## [30] Coxiella sp. DG_40
-## [31] Aquicella lusitana
-## [32] Aquicella siphonis
-## [33] Diplorickettsia massiliensis
-## [34] Candidatus Rickettsiella isopodorum
-## [35] Candidatus Rickettsiella viridis
-## [36] Rickettsiella grylli
-## [37] Candidatus Berkiella aquae
-## [38] Candidatus Berkiella cookevillensis
-## [39] Burkholderia mallei
-## [40] Burkholderia cepacia
-## 73 Levels: Aquicella lusitana ... Rickettsiella grylli
+## [1] Legionella beliardensis Legionella clemsonensis
+## [3] Legionella drancourtii Legionella drozanskii
+## [5] Legionella dumoffii NY23 Legionella endosymbiont of Polyplax serrata PsAG
+## [7] Legionella fairfieldensis Legionella fallonii
+## [9] Legionella gormanii Legionella impletisoli
+## [11] Legionella longbeachae Legionella massiliensis
+## [13] Legionella micdadei Legionella nagasakiensis
+## [15] Legionella norrlandica Legionella pneumophila
+## [17] Legionella rowbothamii Legionella saoudiensis
+## [19] Legionella shakespearei Legionella taurinensis
+## [21] Legionella tunisiensis Legionella wadsworthii
+## [23] Legionella yabuuchiae Candidatus Coxiella mudrowiae
+## [25] Coxiella burnetii Coxiella endosymbiont of Amblyomma americanum
+## [27] Coxiella endosymbiont of Amblyomma sculptum Coxiella endosymbiont of Rhipicephalus microplus
+## [29] Coxiella sp. RIFCSPHIGHO2_12_FULL_42_15 Coxiella sp. DG_40
+## [31] Aquicella lusitana Aquicella siphonis
+## [33] Diplorickettsia massiliensis Candidatus Rickettsiella isopodorum
+## [35] Candidatus Rickettsiella viridis Rickettsiella grylli
+## [37] Candidatus Berkiella aquae Candidatus Berkiella cookevillensis
+## [39] Burkholderia mallei Burkholderia cepacia
+## 73 Levels: Aquicella lusitana Aquicella siphonis Burkholderia cepacia ... Rickettsiella grylli
\end{verbatim}
\begin{alltt}
\hlcom{# only in Burstein}
\hlstd{species[(species} \hlopt{%in%} \hlstd{gupta1}\hlopt{$}\hlstd{Species)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
\end{alltt}
\begin{verbatim}
-## [1] Legionella drozanskii LLAP-1
-## [2] Legionella shakespearei DSM 23087
-## 38 Levels: Fluoribacter dumoffii NY 23 ... Tatlockia micdadei
+## [1] Legionella drozanskii LLAP-1 Legionella shakespearei DSM 23087
+## 38 Levels: Fluoribacter dumoffii NY 23 Fluoribacter gormanii Legionella adelaidensis ... Tatlockia micdadei
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -461,28 +362,18 @@ Final list: Remove Legionella drozanskii and Legionella shakespearei and Aquicel
\hlstd{guptasp[}\hlkwd{grep}\hlstd{(guptasp,} \hlkwc{pattern}\hlstd{=}\hlstr{"Legionella"}\hlstd{)]}
\end{alltt}
\begin{verbatim}
-## [1] Legionella beliardensis
-## [2] Legionella clemsonensis
-## [3] Legionella drancourtii
-## [4] Legionella dumoffii NY23
-## [5] Legionella endosymbiont of Polyplax serrata PsAG
-## [6] Legionella fairfieldensis
-## [7] Legionella fallonii
-## [8] Legionella gormanii
-## [9] Legionella impletisoli
-## [10] Legionella longbeachae
-## [11] Legionella massiliensis
-## [12] Legionella micdadei
-## [13] Legionella nagasakiensis
-## [14] Legionella norrlandica
-## [15] Legionella pneumophila
-## [16] Legionella rowbothamii
-## [17] Legionella saoudiensis
-## [18] Legionella taurinensis
-## [19] Legionella tunisiensis
-## [20] Legionella wadsworthii
+## [1] Legionella beliardensis Legionella clemsonensis
+## [3] Legionella drancourtii Legionella dumoffii NY23
+## [5] Legionella endosymbiont of Polyplax serrata PsAG Legionella fairfieldensis
+## [7] Legionella fallonii Legionella gormanii
+## [9] Legionella impletisoli Legionella longbeachae
+## [11] Legionella massiliensis Legionella micdadei
+## [13] Legionella nagasakiensis Legionella norrlandica
+## [15] Legionella pneumophila Legionella rowbothamii
+## [17] Legionella saoudiensis Legionella taurinensis
+## [19] Legionella tunisiensis Legionella wadsworthii
## [21] Legionella yabuuchiae
-## 73 Levels: Aquicella lusitana ... Rickettsiella grylli
+## 73 Levels: Aquicella lusitana Aquicella siphonis Burkholderia cepacia ... Rickettsiella grylli
\end{verbatim}
\begin{alltt}
\hlcom{## Keep only legio and coxiella}
@@ -515,44 +406,25 @@ Manual research of reference genomes using gupta1
\hlstd{guptaonly[,}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{5}\hlstd{,}\hlnum{6}\hlstd{)]}
\end{alltt}
\begin{verbatim}
-## Species
-## 3 Legionella beliardensis
-## 9 Legionella clemsonensis
-## 10 Legionella drancourtii
-## 13 Legionella endosymbiont of Polyplax serrata PsAG
-## 15 Legionella fairfieldensis
-## 16 Legionella fallonii
-## 22 Legionella impletisoli
-## 28 Legionella longbeachae
-## 30 Legionella massiliensis
-## 33 Legionella nagasakiensis
-## 35 Legionella norrlandica
-## 41 Legionella rowbothamii
-## 45 Legionella saoudiensis
-## 50 Legionella taurinensis
-## 52 Legionella tunisiensis
-## 53 Legionella wadsworthii
-## 56 Legionella yabuuchiae
-## 58 Coxiella burnetii
-## Number_of_Assemblies
-## 3 2
-## 9 1
-## 10 1
-## 13 1
-## 15 2
-## 16 1
-## 22 1
-## 28 9
-## 30 2
-## 33 1
-## 35 1
-## 41 1
-## 45 1
-## 50 16
-## 52 1
-## 53 3
-## 56 1
-## 58 69
+## Species Number_of_Assemblies
+## 3 Legionella beliardensis 2
+## 9 Legionella clemsonensis 1
+## 10 Legionella drancourtii 1
+## 13 Legionella endosymbiont of Polyplax serrata PsAG 1
+## 15 Legionella fairfieldensis 2
+## 16 Legionella fallonii 1
+## 22 Legionella impletisoli 1
+## 28 Legionella longbeachae 9
+## 30 Legionella massiliensis 2
+## 33 Legionella nagasakiensis 1
+## 35 Legionella norrlandica 1
+## 41 Legionella rowbothamii 1
+## 45 Legionella saoudiensis 1
+## 50 Legionella taurinensis 16
+## 52 Legionella tunisiensis 1
+## 53 Legionella wadsworthii 3
+## 56 Legionella yabuuchiae 1
+## 58 Coxiella burnetii 69
## Available_Genome_Accession_Number_.Ref_Seq_is_provided_when_available.
## 3 NZ_UGNV01000001.1
## 9 NZ_CP016397.1
@@ -688,7 +560,7 @@ From a list given by Margaux Pillon
\item Legionella septentrionalis GCF-003990055.1 GCA\_003990055.1 Ok
\item Legionella donaldsonii GFC-900452385.1 GCA\_900452385.1 Ok
\item L. pneumophila fraseri Dallas1E CP017458.1 GCA\_001886835.1 OK
- \item L. pneumophila fraseri Lansing 3 CP021257.1 GCA\_003003865.1 Ok
+ \item L. pneumophila fraseri Lansing 3 CP021257.1 GCA\_003003865.1 Ok
\item L. pneumophila fraseri Los Angeles 1 CP021265.1 GCA\_003003755.1 Ok
\end{itemize}
@@ -765,38 +637,25 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p
\begin{alltt}
\hlkwd{library}\hlstd{(ape)}
-\hlstd{aln}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"fasta/78Lp/"}\hlstd{)}
+\hlstd{aln}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"fasta/78Lp_V2/"}\hlstd{)}
\hlstd{subrep}\hlkwb{<-}\hlkwd{list.files}\hlstd{(aln)}
\hlstd{subrep}\hlkwb{<-}\hlstd{subrep[}\hlkwd{grep}\hlstd{(}\hlkwc{x}\hlstd{=subrep,} \hlkwc{pattern}\hlstd{=}\hlstr{"Q5"}\hlstd{)]}
\hlstd{subrep}
\end{alltt}
\begin{verbatim}
-## [1] "Q5ZRF4_lpg2928" "Q5ZRP4_lpg2836" "Q5ZRQ7_lpg2823"
-## [4] "Q5ZRT6_lpg2792" "Q5ZRV3_lpg2773" "Q5ZRV4_lpg2772"
-## [7] "Q5ZRV6_lpg2770" "Q5ZRW1_lpg2765" "Q5ZRX2_lpg2754"
-## [10] "Q5ZRZ3_lpg2727" "Q5ZS05_lpg2714" "Q5ZS08_lpg2711"
-## [13] "Q5ZS49_lpg2670" "Q5ZS63_lpg2656" "Q5ZS65_lpg2654"
-## [16] "Q5ZT28_lpg2337" "Q5ZT35_lpg2330" "Q5ZT51_lpg2314"
-## [19] "Q5ZT61_lpg2304" "Q5ZT63_lpg2302" "Q5ZTX1_lpg2037"
-## [22] "Q5ZTX7_lpg2031" "Q5ZU05_lpg2003" "Q5ZU96_lpg1911"
-## [25] "Q5ZUH7_lpg1821" "Q5ZUJ7_lpg1801" "Q5ZUM6_lpg1767"
-## [28] "Q5ZUS0_lpg1722" "Q5ZUS8_lpg1714" "Q5ZUT0_lpg1712"
-## [31] "Q5ZVH3_lpg1467" "Q5ZVJ6_lpg1444" "Q5ZVJ7_lpg1443"
-## [34] "Q5ZVL5_lpg1425" "Q5ZVP0_lpg1400" "Q5ZVP1_lpg1399"
-## [37] "Q5ZVU2_lpg1348" "Q5ZVV6_lpg1334" "Q5ZVY2_lpg1306"
-## [40] "Q5ZWA4_lpg1181" "Q5ZWZ6_lpg0937" "Q5ZXE5_lpg0786"
-## [43] "Q5ZXJ7_lpg0734" "Q5ZXK6_lpg0725" "Q5ZXL2_lpg0719"
-## [46] "Q5ZXN3_lpg0698" "Q5ZXP3_lpg0688" "Q5ZXP6_lpg0685"
-## [49] "Q5ZXZ2_lpg0588" "Q5ZY30_lpg0543" "Q5ZY59_lpg0513"
-## [52] "Q5ZY67_lpg0505" "Q5ZY69_lpg0503" "Q5ZYH2_lpg0400"
-## [55] "Q5ZYL9_lpg0353" "Q5ZYM1_lpg0351" "Q5ZYM4_lpg0348"
-## [58] "Q5ZYM6_lpg0346" "Q5ZYM7_lpg0345" "Q5ZYM8_lpg0344"
-## [61] "Q5ZYM9_lpg0343" "Q5ZYN1_lpg0341" "Q5ZYN4_lpg0338"
-## [64] "Q5ZYN6_lpg0336" "Q5ZYN7_lpg0335" "Q5ZYN8_lpg0334"
-## [67] "Q5ZYP0_lpg0332" "Q5ZYP1_lpg0331" "Q5ZYP2_lpg0330"
-## [70] "Q5ZYP3_lpg0329" "Q5ZYP4_lpg0328" "Q5ZYP7_lpg0325"
-## [73] "Q5ZYQ0_lpg0322" "Q5ZYQ3_lpg0319" "Q5ZYQ4_lpg0318"
-## [76] "Q5ZYQ5_lpg0317" "Q5ZYS4_lpg0287"
+## [1] "Q5ZRF4_lpg2928" "Q5ZRP4_lpg2836" "Q5ZRQ7_lpg2823" "Q5ZRT6_lpg2792" "Q5ZRV3_lpg2773" "Q5ZRV4_lpg2772"
+## [7] "Q5ZRV6_lpg2770" "Q5ZRW1_lpg2765" "Q5ZRX2_lpg2754" "Q5ZRZ3_lpg2727" "Q5ZS05_lpg2714" "Q5ZS08_lpg2711"
+## [13] "Q5ZS49_lpg2670" "Q5ZS63_lpg2656" "Q5ZS65_lpg2654" "Q5ZT28_lpg2337" "Q5ZT35_lpg2330" "Q5ZT51_lpg2314"
+## [19] "Q5ZT61_lpg2304" "Q5ZT63_lpg2302" "Q5ZTX1_lpg2037" "Q5ZTX7_lpg2031" "Q5ZU05_lpg2003" "Q5ZU96_lpg1911"
+## [25] "Q5ZUH7_lpg1821" "Q5ZUJ7_lpg1801" "Q5ZUM6_lpg1767" "Q5ZUS0_lpg1722" "Q5ZUS8_lpg1714" "Q5ZUT0_lpg1712"
+## [31] "Q5ZVH3_lpg1467" "Q5ZVJ6_lpg1444" "Q5ZVJ7_lpg1443" "Q5ZVL5_lpg1425" "Q5ZVP0_lpg1400" "Q5ZVP1_lpg1399"
+## [37] "Q5ZVU2_lpg1348" "Q5ZVV6_lpg1334" "Q5ZVY2_lpg1306" "Q5ZWA4_lpg1181" "Q5ZWZ6_lpg0937" "Q5ZXE5_lpg0786"
+## [43] "Q5ZXJ7_lpg0734" "Q5ZXK6_lpg0725" "Q5ZXL2_lpg0719" "Q5ZXN3_lpg0698" "Q5ZXP3_lpg0688" "Q5ZXP6_lpg0685"
+## [49] "Q5ZXZ2_lpg0588" "Q5ZY30_lpg0543" "Q5ZY59_lpg0513" "Q5ZY67_lpg0505" "Q5ZY69_lpg0503" "Q5ZYH2_lpg0400"
+## [55] "Q5ZYL9_lpg0353" "Q5ZYM1_lpg0351" "Q5ZYM4_lpg0348" "Q5ZYM6_lpg0346" "Q5ZYM7_lpg0345" "Q5ZYM8_lpg0344"
+## [61] "Q5ZYM9_lpg0343" "Q5ZYN1_lpg0341" "Q5ZYN4_lpg0338" "Q5ZYN6_lpg0336" "Q5ZYN7_lpg0335" "Q5ZYN8_lpg0334"
+## [67] "Q5ZYP0_lpg0332" "Q5ZYP1_lpg0331" "Q5ZYP2_lpg0330" "Q5ZYP3_lpg0329" "Q5ZYP4_lpg0328" "Q5ZYP7_lpg0325"
+## [73] "Q5ZYQ0_lpg0322" "Q5ZYQ3_lpg0319" "Q5ZYQ4_lpg0318" "Q5ZYQ5_lpg0317" "Q5ZYS4_lpg0287"
\end{verbatim}
\begin{alltt}
\hlstd{cat}\hlkwb{<-}\hlkwd{vector}\hlstd{()}
@@ -811,8 +670,10 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p
\hlstd{file}\hlkwb{<-}\hlstd{file[}\hlkwd{grep}\hlstd{(}\hlkwc{x}\hlstd{=file,} \hlkwc{pattern}\hlstd{=}\hlstr{"aln"}\hlstd{)]}
\hlkwa{if} \hlstd{(}\hlkwd{length}\hlstd{(file)}\hlopt{>}\hlnum{0}\hlstd{)\{}
\hlstd{fasta}\hlkwb{<-}\hlkwd{read.dna}\hlstd{(}\hlkwd{paste0}\hlstd{(aln,} \hlstr{"/"}\hlstd{,subrepcurrent,} \hlstr{"/"}\hlstd{, file),} \hlkwc{format}\hlstd{=}\hlstr{"fasta"}\hlstd{,} \hlkwc{as.character}\hlstd{=}\hlnum{TRUE}\hlstd{)}
- \hlkwd{rownames}\hlstd{(fasta)}\hlkwb{<-}\hlkwd{sapply}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta),} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)} \hlkwd{strsplit}\hlstd{(x,} \hlkwc{split}\hlstd{=}\hlstr{"."}\hlstd{,} \hlkwc{fixed}\hlstd{=}\hlnum{TRUE}\hlstd{)[[}\hlnum{1}\hlstd{]][}\hlnum{1}\hlstd{])}
- \hlstd{cat}\hlkwb{<-}\hlkwd{c}\hlstd{(cat,} \hlkwd{rownames}\hlstd{(fasta))}
+ \hlstd{tmprownames}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}\hlkwd{grepl}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta),} \hlkwc{pattern} \hlstd{=} \hlstr{"pneumo"}\hlstd{),}
+ \hlkwd{substr}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta)[}\hlkwd{grep}\hlstd{(}\hlkwc{pattern} \hlstd{=} \hlstr{"pneumophila"}\hlstd{,}\hlkwd{rownames}\hlstd{(fasta))],} \hlnum{1}\hlstd{,}\hlnum{31}\hlstd{),}
+ \hlkwd{sapply}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta),} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)} \hlkwd{strsplit}\hlstd{(x,} \hlkwc{split}\hlstd{=}\hlstr{"."}\hlstd{,} \hlkwc{fixed}\hlstd{=}\hlnum{TRUE}\hlstd{)[[}\hlnum{1}\hlstd{]][}\hlnum{1}\hlstd{]))}
+ \hlstd{cat}\hlkwb{<-}\hlkwd{c}\hlstd{(cat, tmprownames)}
\hlstd{\}}
\hlstd{\}}
\end{alltt}
@@ -907,97 +768,21 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p
\hlcom{# make a cat list containing all species names}
\hlkwa{for} \hlstd{(subrepcurrent} \hlkwa{in} \hlstd{subrep)\{}
-\hlkwd{print}\hlstd{(subrepcurrent)}
+\hlcom{#print(subrepcurrent)}
\hlstd{file}\hlkwb{<-}\hlkwd{list.files}\hlstd{(}\hlkwd{paste0}\hlstd{(aln,} \hlstr{"/"}\hlstd{, subrepcurrent))}
\hlstd{file}\hlkwb{<-}\hlstd{file[}\hlkwd{grep}\hlstd{(}\hlkwc{x}\hlstd{=file,} \hlkwc{pattern}\hlstd{=}\hlstr{"aln"}\hlstd{)]}
\hlkwa{if} \hlstd{(}\hlkwd{length}\hlstd{(file)}\hlopt{>}\hlnum{0}\hlstd{)\{}
\hlstd{fasta}\hlkwb{<-}\hlkwd{read.dna}\hlstd{(}\hlkwd{paste0}\hlstd{(aln,} \hlstr{"/"}\hlstd{,subrepcurrent,} \hlstr{"/"}\hlstd{, file),} \hlkwc{format}\hlstd{=}\hlstr{"fasta"}\hlstd{,} \hlkwc{as.character}\hlstd{=}\hlnum{TRUE}\hlstd{)}
- \hlkwd{rownames}\hlstd{(fasta)}\hlkwb{<-}\hlkwd{sapply}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta),} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)} \hlkwd{strsplit}\hlstd{(x,} \hlkwc{split}\hlstd{=}\hlstr{"."}\hlstd{,} \hlkwc{fixed}\hlstd{=}\hlnum{TRUE}\hlstd{)[[}\hlnum{1}\hlstd{]][}\hlnum{1}\hlstd{])}
- \hlstd{tmp}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}\hlkwd{rownames}\hlstd{(tab)} \hlopt{%in%} \hlkwd{rownames}\hlstd{(fasta),} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+ \hlstd{tmprownames}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}\hlkwd{grepl}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta),} \hlkwc{pattern} \hlstd{=} \hlstr{"pneumo"}\hlstd{),}
+ \hlkwd{substr}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta)[}\hlkwd{grep}\hlstd{(}\hlkwc{pattern} \hlstd{=} \hlstr{"pneumophila"}\hlstd{,}\hlkwd{rownames}\hlstd{(fasta))],} \hlnum{1}\hlstd{,}\hlnum{31}\hlstd{),}
+ \hlkwd{sapply}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta),} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)} \hlkwd{strsplit}\hlstd{(x,} \hlkwc{split}\hlstd{=}\hlstr{"."}\hlstd{,} \hlkwc{fixed}\hlstd{=}\hlnum{TRUE}\hlstd{)[[}\hlnum{1}\hlstd{]][}\hlnum{1}\hlstd{]))}
+
+ \hlstd{tmp}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}\hlkwd{rownames}\hlstd{(tab)} \hlopt{%in%} \hlstd{tmprownames,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
\hlstd{tab[,subrepcurrent]}\hlkwb{<-}\hlstd{tmp}
\hlstd{\}}
\hlstd{\}}
\end{alltt}
-\begin{verbatim}
-## [1] "Q5ZRF4_lpg2928"
-## [1] "Q5ZRP4_lpg2836"
-## [1] "Q5ZRQ7_lpg2823"
-## [1] "Q5ZRT6_lpg2792"
-## [1] "Q5ZRV3_lpg2773"
-## [1] "Q5ZRV4_lpg2772"
-## [1] "Q5ZRV6_lpg2770"
-## [1] "Q5ZRW1_lpg2765"
-## [1] "Q5ZRX2_lpg2754"
-## [1] "Q5ZRZ3_lpg2727"
-## [1] "Q5ZS05_lpg2714"
-## [1] "Q5ZS08_lpg2711"
-## [1] "Q5ZS49_lpg2670"
-## [1] "Q5ZS63_lpg2656"
-## [1] "Q5ZS65_lpg2654"
-## [1] "Q5ZT28_lpg2337"
-## [1] "Q5ZT35_lpg2330"
-## [1] "Q5ZT51_lpg2314"
-## [1] "Q5ZT61_lpg2304"
-## [1] "Q5ZT63_lpg2302"
-## [1] "Q5ZTX1_lpg2037"
-## [1] "Q5ZTX7_lpg2031"
-## [1] "Q5ZU05_lpg2003"
-## [1] "Q5ZU96_lpg1911"
-## [1] "Q5ZUH7_lpg1821"
-## [1] "Q5ZUJ7_lpg1801"
-## [1] "Q5ZUM6_lpg1767"
-## [1] "Q5ZUS0_lpg1722"
-## [1] "Q5ZUS8_lpg1714"
-## [1] "Q5ZUT0_lpg1712"
-## [1] "Q5ZVH3_lpg1467"
-## [1] "Q5ZVJ6_lpg1444"
-## [1] "Q5ZVJ7_lpg1443"
-## [1] "Q5ZVL5_lpg1425"
-## [1] "Q5ZVP0_lpg1400"
-## [1] "Q5ZVP1_lpg1399"
-## [1] "Q5ZVU2_lpg1348"
-## [1] "Q5ZVV6_lpg1334"
-## [1] "Q5ZVY2_lpg1306"
-## [1] "Q5ZWA4_lpg1181"
-## [1] "Q5ZWZ6_lpg0937"
-## [1] "Q5ZXE5_lpg0786"
-## [1] "Q5ZXJ7_lpg0734"
-## [1] "Q5ZXK6_lpg0725"
-## [1] "Q5ZXL2_lpg0719"
-## [1] "Q5ZXN3_lpg0698"
-## [1] "Q5ZXP3_lpg0688"
-## [1] "Q5ZXP6_lpg0685"
-## [1] "Q5ZXZ2_lpg0588"
-## [1] "Q5ZY30_lpg0543"
-## [1] "Q5ZY59_lpg0513"
-## [1] "Q5ZY67_lpg0505"
-## [1] "Q5ZY69_lpg0503"
-## [1] "Q5ZYH2_lpg0400"
-## [1] "Q5ZYL9_lpg0353"
-## [1] "Q5ZYM1_lpg0351"
-## [1] "Q5ZYM4_lpg0348"
-## [1] "Q5ZYM6_lpg0346"
-## [1] "Q5ZYM7_lpg0345"
-## [1] "Q5ZYM8_lpg0344"
-## [1] "Q5ZYM9_lpg0343"
-## [1] "Q5ZYN1_lpg0341"
-## [1] "Q5ZYN4_lpg0338"
-## [1] "Q5ZYN6_lpg0336"
-## [1] "Q5ZYN7_lpg0335"
-## [1] "Q5ZYN8_lpg0334"
-## [1] "Q5ZYP0_lpg0332"
-## [1] "Q5ZYP1_lpg0331"
-## [1] "Q5ZYP2_lpg0330"
-## [1] "Q5ZYP3_lpg0329"
-## [1] "Q5ZYP4_lpg0328"
-## [1] "Q5ZYP7_lpg0325"
-## [1] "Q5ZYQ0_lpg0322"
-## [1] "Q5ZYQ3_lpg0319"
-## [1] "Q5ZYQ4_lpg0318"
-## [1] "Q5ZYQ5_lpg0317"
-## [1] "Q5ZYS4_lpg0287"
-\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -1032,7 +817,7 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlstd{treepath}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"fasta/78Lp/cat.phylip_phyml_tree"}\hlstd{)}
+\hlstd{treepath}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"fasta/78Lp_V2/cat.phylip_phyml_tree"}\hlstd{)}
\hlstd{tree}\hlkwb{<-}\hlkwd{read.tree}\hlstd{(treepath)}
\hlkwd{plot}\hlstd{(}\hlkwd{root}\hlstd{(tree,} \hlkwc{outgroup} \hlstd{=} \hlstr{"Coxiella_burnetii"}\hlstd{))}
diff --git a/doc/1_reference_legio_phylo.toc b/doc/1_reference_legio_phylo.toc
index 9ddeec57f032e7952b8dabb2229f5477809e463c..8d6b229d571384426462159c68e9e9f4dd52e108 100644
--- a/doc/1_reference_legio_phylo.toc
+++ b/doc/1_reference_legio_phylo.toc
@@ -2,11 +2,11 @@
\contentsline {subsection}{\numberline {1.1}Objective}{2}{subsection.1.1}
\contentsline {subsection}{\numberline {1.2}Data}{2}{subsection.1.2}
\contentsline {subsubsection}{\numberline {1.2.1}Data from the first publication:}{2}{subsubsection.1.2.1}
-\contentsline {subsubsection}{\numberline {1.2.2}Data from the seconde publication:}{5}{subsubsection.1.2.2}
-\contentsline {subsubsection}{\numberline {1.2.3}Data from Legionella pneumophila reference strains:}{13}{subsubsection.1.2.3}
-\contentsline {subsection}{\numberline {1.3}Add missing species}{14}{subsection.1.3}
-\contentsline {section}{\numberline {2}Get genes sequences}{15}{section.2}
-\contentsline {subsection}{\numberline {2.1}Get sequences from Burstein et al.}{15}{subsection.2.1}
-\contentsline {section}{\numberline {3}Phylogeny}{16}{section.3}
-\contentsline {subsection}{\numberline {3.1}Genes alignement}{16}{subsection.3.1}
-\contentsline {subsection}{\numberline {3.2}Concatenate and Supertree}{26}{subsection.3.2}
+\contentsline {subsubsection}{\numberline {1.2.2}Data from the seconde publication:}{4}{subsubsection.1.2.2}
+\contentsline {subsubsection}{\numberline {1.2.3}Data from Legionella pneumophila reference strains:}{10}{subsubsection.1.2.3}
+\contentsline {subsection}{\numberline {1.3}Add missing species}{11}{subsection.1.3}
+\contentsline {section}{\numberline {2}Get genes sequences}{12}{section.2}
+\contentsline {subsection}{\numberline {2.1}Get sequences from Burstein et al.}{12}{subsection.2.1}
+\contentsline {section}{\numberline {3}Phylogeny}{13}{section.3}
+\contentsline {subsection}{\numberline {3.1}Genes alignement}{13}{subsection.3.1}
+\contentsline {subsection}{\numberline {3.2}Concatenate and Supertree}{20}{subsection.3.2}
diff --git a/doc/figure/barplot1-1.pdf b/doc/figure/barplot1-1.pdf
index 34e0f2e43d97be30677201ffdfb42ea4be02624e..a65db9c6d3bf74bd04e51e4485322237791085de 100644
Binary files a/doc/figure/barplot1-1.pdf and b/doc/figure/barplot1-1.pdf differ
diff --git a/doc/figure/barplot2-1.pdf b/doc/figure/barplot2-1.pdf
index 26ccb10e11a1252c6a5471364392cca8efb7a6fd..116e2325df3f91294dc3d2eb257d9112c3c7cb97 100644
Binary files a/doc/figure/barplot2-1.pdf and b/doc/figure/barplot2-1.pdf differ
diff --git a/doc/figure/tree-1.pdf b/doc/figure/tree-1.pdf
index c82de6dd7583a9703197358968247c2427bd6d9b..3ac19479d557572bb3576b65a6a00e682505cc4a 100644
Binary files a/doc/figure/tree-1.pdf and b/doc/figure/tree-1.pdf differ
diff --git a/doc/tabAss_V2.txt b/doc/tabAss_V2.txt
index 2fcfba9a87a37179ebbb2f30874c9a03fc5af2bc..3c75a28d7f30c435226dc2239aef40f7d7b199d3 100644
--- a/doc/tabAss_V2.txt
+++ b/doc/tabAss_V2.txt
@@ -64,7 +64,6 @@ GCA_900461525.1;Legionella busanensis;Pillon
GCA_000236145.1;Legionella dumoffi;Pillon
GCA_003990055.1;Legionella septentrionalis;Pillon
GCA_900452385.1;Legionella donaldsonii;Pillon
-GCA_001648685.1;Legionella gormannii;Pillon
GCA_001886835.1;Legionella fraseri Dallas1E;Pillon
GCA_003003865.1;Legionella fraseri Lansing 3;Pillon
GCA_003003755.1;Legionella fraseri Los Angeles 1;Pillon