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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+This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex 2021.6.16)  25 JAN 2022 10:21
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+Overfull \hbox (295.3504pt too wide) in paragraph at lines 133--133
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+LaTeX Font Info:    Try loading font information for OMS+cmtt on input line 140
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+Overfull \hbox (243.33853pt too wide) in paragraph at lines 140--140
 [][]\OT1/cmtt/m/n/10.95 tab1[][]<-[][]read.table[][]([][]paste0[][](data, datal
 ist1[[][]1[][]]),[] []skip[][]=[][]2[][],[] []sep[][]=[][]"\OMS/cmsy/m/n/10.95 
 n\OT1/cmtt/m/n/10.95 t"[][],[] []fill[][]=[][]TRUE[][],[] []header[][]=[][]TRUE
@@ -786,10 +833,53 @@ n\OT1/cmtt/m/n/10.95 t"[][],[] []fill[][]=[][]TRUE[][],[] []header[][]=[][]TRUE
  []
 
 
-Package xcolor Warning: Incompatible color definition on input line 178.
+Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+[]\OT1/cmtt/m/n/10.95 ##              Species ATCC.number Strain.designation   
+                                 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.
 
-Overfull \hbox (392.80441pt too wide) in paragraph at lines 180--180
+
+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]
+
+Package xcolor Warning: Incompatible color definition on input line 207.
+
+
+Package xcolor Warning: Incompatible color definition on input line 219.
+
+
+Overfull \hbox (208.8464pt too wide) in paragraph at lines 229--229
 [][]\OT1/cmtt/m/n/10.95 gupta1[][]<-[][]read.table[][]([][]paste0[][](data, dat
 alist2[[][]1[][]]),[] []sep[][]=[][]"\OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/n/10.95 t
 "[][],[] []fill[][]=[][]TRUE[][],[] []header[][]=[][]TRUE[][],[] []comment.char
@@ -825,181 +987,505 @@ alist2[[][]1[][]]),[] []sep[][]=[][]"\OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/n/10.95 t
  []
 
 
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-[]\OT1/cmtt/m/n/10.95 ##                                                       
-                 Type.Strain[] 
+Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255
+[]\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
-03645; DSM 19888; NCTC 12735[] 
+Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255
+[]\OT1/cmtt/m/n/10.95 ## 1    Legionella adelaidensis          1762-Aus-E; ATCC
+ 49625; CCUG 31231 A; CIP 103645; DSM 19888; NCTC 12735[] 
  []
 
 
-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
- 7573; NCTC 11974; WA-316-C3[] 
+Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255
+[]\OT1/cmtt/m/n/10.95 ## 2           Legionella anisa   ATCC 35292; CCUG 29665;
+ CIP 103870; DSM 17627; JCM 7573; NCTC 11974; WA-316-C3[] 
  []
 
 
-Overfull \hbox (128.63846pt too wide) in paragraph at lines 302--302
-[]\OT1/cmtt/m/n/10.95 ## 3         ATCC 700512; CIP 106632; DSM 19152; Montb\xe
-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 
+106632; DSM 19152; Montb\xe9liard A1; Montb\xe9liard A1[] 
  []
 
 
-Overfull \hbox (128.63846pt too wide) in paragraph at lines 302--302
-[]\OT1/cmtt/m/n/10.95 ## 4 1407-AL-H; ATCC 43702; CCUG 31233 A; CIP 103871; DSM
- 19232; JCM 7559; NCTC 12437[] 
+Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255
+[]\OT1/cmtt/m/n/10.95 ## 4 Legionella birminghamensis 1407-AL-H; ATCC 43702; CC
+UG 31233 A; CIP 103871; DSM 19232; JCM 7559; NCTC 12437[] 
  []
 
 
-Overfull \hbox (128.63846pt too wide) in paragraph at lines 302--302
-[]\OT1/cmtt/m/n/10.95 ## 5                                   ALLO1; ATCC 33217;
- CIP 103872; DSM 16523; WIGA[] 
+Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255
+[]\OT1/cmtt/m/n/10.95 ## 5       Legionella bozemanae                          
+         ALLO1; ATCC 33217; CIP 103872; DSM 16523; WIGA[] 
  []
 
 
-Overfull \hbox (128.63846pt too wide) in paragraph at lines 302--302
-[]\OT1/cmtt/m/n/10.95 ## 6                 441-1; ATCC 43878; CCUG 31114; CIP 1
-03874; DSM 19236; NCTC 12240[] 
+Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255
+[]\OT1/cmtt/m/n/10.95 ## 6       Legionella brunensis                 441-1; AT
+CC 43878; CCUG 31114; CIP 103874; DSM 19236; NCTC 12240[] 
  []
 
 
-Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302
+Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ##   Type.Strain.chosen Type_Strain_Availability Number_o
 f_Assemblies[] 
  []
 
 
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+Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ## 1         1762-Aus-E                        Y         
            3[] 
  []
 
 
-Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302
+Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ## 2               <NA>                        N         
            5[] 
  []
 
 
-Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302
+Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ## 3               <NA>                        N         
            2[] 
  []
 
 
-Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302
+Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ## 4          1407-AL-H                        Y         
            3[] 
  []
 
 
-Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302
+Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ## 5               WIGA                        Y         
            5[] 
  []
 
 
-Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302
+Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ## 6         ATCC 43878                        Y         
            2[] 
  []
 
 
-Overfull \hbox (71.15158pt too wide) in paragraph at lines 302--302
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 []\OT1/cmtt/m/n/10.95 ##   Available_Genome_Accession_Number_.Ref_Seq_is_provid
 ed_when_available.[] 
  []
 
 
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+Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ## 1                                                   NZ
 _CAAAHS000000000.1[] 
  []
 
 
-Overfull \hbox (71.15158pt too wide) in paragraph at lines 302--302
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ## 2                                                     
      NZ_CP029563.1[] 
  []
 
 
-Overfull \hbox (71.15158pt too wide) in paragraph at lines 302--302
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ## 3                                                     
  NZ_UGNV01000001.1[] 
  []
 
 
-Overfull \hbox (71.15158pt too wide) in paragraph at lines 302--302
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ## 4                                                     
  NZ_LNXT00000000.1[] 
  []
 
 
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+Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ## 5                                                     
  NZ_LNXU01000019.1[] 
  []
 
 
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+Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255
 []\OT1/cmtt/m/n/10.95 ## 6                                                     
  NZ_LNXV01000029.1[] 
  []
 
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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]
 
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+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][][
 ] 
  []
 
 
-Overfull \hbox (42.40814pt too wide) in paragraph at lines 489--489
+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]
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ##                                             Species Nu
+mber_of_Assemblies[] 
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\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[] 
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\OT1/cmtt/m/n/10.95 ## 10                           Legionella drancourtii   
+                 1[] 
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\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[] 
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\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[] 
+ []
+
+
+Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447
+[]\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[] 
+ []
+
+
+Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447
 []\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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+Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447
 []\OT1/cmtt/m/n/10.95 ## 9                                                     
       NZ_CP016397.1[] 
  []
 
 
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+Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447
 []\OT1/cmtt/m/n/10.95 ## 10                                                    
       NZ_JH413847.1[] 
  []
 
 
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+Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447
 []\OT1/cmtt/m/n/10.95 ## 13                                                    
       NZ_CP021497.1[] 
  []
 
 
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+Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447
 []\OT1/cmtt/m/n/10.95 ## 15                                                    
   NZ_JHYC01000001.1[] 
  []
 
 
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+Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447
 []\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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+Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447
 []\OT1/cmtt/m/n/10.95 ## 28                                                    
         NC_013861.1[] 
  []
 
 
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+Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447
 []\OT1/cmtt/m/n/10.95 ## 30                                                    
   NZ_CCVW01000001.1[] 
  []
 
 
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+Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447
 []\OT1/cmtt/m/n/10.95 ## 33                                                   N
 Z_CAAAID010000001.1[] 
  []
 
 
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+Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447
 []\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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 []\OT1/cmtt/m/n/10.95 ## 45                                                    
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 []\OT1/cmtt/m/n/10.95 ## 50                                                    
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 []\OT1/cmtt/m/n/10.95 ## 52                                                    
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 []\OT1/cmtt/m/n/10.95 ## 53                                                    
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 []\OT1/cmtt/m/n/10.95 ## 56                                                   N
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 []\OT1/cmtt/m/n/10.95 ## 58                                                    
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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