Commit e971674a authored by mcariou's avatar mcariou
Browse files

add genomes

parent c6dc77df
......@@ -197,5 +197,29 @@ Not sure if this works for unique genes.
- Revoir le script qui génère la banque proteic pour le rendre utilisable plus généralement.
**Missing species**
- Legionella micdadei GCF-001467875.1 GCA_001467875.1 Tatlockia micdadei
- Legionella gresilensis GCF_900639865.1 GCA_900639865.1 OK
- Legionella busanensis GCF-900431525.1 GCA_900461525.1 OK
- Legionella dumoffi GCF-000236145.1 GCA_000236145.1 Fluoribacter dumoffii
- Legionella gormanii GCF-001648885.1 Fluoribacter
gormanii
- Legionella septentrionalis GCF-003990055.1 GCA_003990055.1 Ok
- Legionella donaldsonii GFC-900452385.1 GCA_900452385.1 Ok
- L. pneumophila fraseri Dallas1E CP017458.1 GCA_001886835.1 OK
- L. pneumophila fraseri Lansing 3 CP021257.1 GCA_003003865.1 Ok
- L. pneumophila fraseri Los Angeles 1 CP021265.1 GCA_003003755.1 Ok
......@@ -258,6 +258,45 @@ tabAss<-rbind(tabAss, cbind(Taxonomy, Assembly, Origin))
write.table(tabAss, paste0(home, "/phylolegio/doc/tabAss.txt"), quote=FALSE, row.names=FALSE, sep=";")
@
\subsection{Add missing species}
From a list given by Margaux Pillon
\begin{itemize}
\item Legionella micdadei GCF-001467875.1 "GCA\_001467875.1" Tatlockia micdadei
\item Legionella gresilensis GCF\_900639865.1 GCA\_900639865.1 OK
\item Legionella busanensis GCF-900431525.1 GCA\_900461525.1 OK
\item Legionella dumoffi GCF-000236145.1 GCA\_000236145.1 Fluoribacter dumoffii
\item Legionella gormanii GCF-001648885.1 Fluoribacter gormanii
\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 Los Angeles 1 CP021265.1 GCA\_003003755.1 Ok
\end{itemize}
<<>>=
tabAss$Assembly<-as.character(tabAss$Assembly)
tabAss$Taxonomy<-as.character(tabAss$Taxonomy)
tabAss$Origin<-as.character(tabAss$Origin)
tabAss_V2<-rbind(tabAss, c("GCA_001467875.1", "Legionella micdadei", "Pillon"))
tabAss_V2<-rbind(tabAss_V2, c("GCA_900639865.1", "Legionella gresilensis", "Pillon"))
tabAss_V2<-rbind(tabAss_V2, c("GCA_900461525.1", "Legionella busanensis", "Pillon"))
tabAss_V2<-rbind(tabAss_V2, c("GCA_000236145.1", "Legionella dumoffi", "Pillon"))
tabAss_V2<-rbind(tabAss_V2, c("GCA_003990055.1", "Legionella septentrionalis", "Pillon"))
tabAss_V2<-rbind(tabAss_V2, c("GCA_900452385.1", "Legionella donaldsonii", "Pillon"))
tabAss_V2<-rbind(tabAss_V2, c("GCA_001886835.1", "Legionella fraseri Dallas1E", "Pillon"))
tabAss_V2<-rbind(tabAss_V2, c("GCA_003003865.1", "Legionella fraseri Lansing 3", "Pillon"))
tabAss_V2<-rbind(tabAss_V2, c("GCA_003003755.1", "Legionella fraseri Los Angeles 1", "Pillon"))
#Legionella gormanii GCF-001648885.1 Fluoribacter gormanii
write.table(tabAss_V2, paste0(home, "/phylolegio/doc/tabAss_V2.txt"), quote=FALSE, row.names=FALSE, sep=";")
@
\section{Get genes sequences}
......
......@@ -20,10 +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:}{4}{subsubsection.1.2.2}}
\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.3}Data from Legionella pneumophila reference strains:}{11}{subsubsection.1.2.3}}
\@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}{23}{subsection.3.2}}
\@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}}
This diff is collapsed.
......@@ -4,8 +4,9 @@
\BOOKMARK [3][-]{subsubsection.1.2.1}{Data from the first publication:}{subsection.1.2}% 4
\BOOKMARK [3][-]{subsubsection.1.2.2}{Data from the seconde publication:}{subsection.1.2}% 5
\BOOKMARK [3][-]{subsubsection.1.2.3}{Data from Legionella pneumophila reference strains:}{subsection.1.2}% 6
\BOOKMARK [1][-]{section.2}{Get genes sequences}{}% 7
\BOOKMARK [2][-]{subsection.2.1}{Get sequences from Burstein et al.}{section.2}% 8
\BOOKMARK [1][-]{section.3}{Phylogeny}{}% 9
\BOOKMARK [2][-]{subsection.3.1}{Genes alignement}{section.3}% 10
\BOOKMARK [2][-]{subsection.3.2}{Concatenate and Supertree}{section.3}% 11
\BOOKMARK [2][-]{subsection.1.3}{Add missing species}{section.1}% 7
\BOOKMARK [1][-]{section.2}{Get genes sequences}{}% 8
\BOOKMARK [2][-]{subsection.2.1}{Get sequences from Burstein et al.}{section.2}% 9
\BOOKMARK [1][-]{section.3}{Phylogeny}{}% 10
\BOOKMARK [2][-]{subsection.3.1}{Genes alignement}{section.3}% 11
\BOOKMARK [2][-]{subsection.3.2}{Concatenate and Supertree}{section.3}% 12
This diff is collapsed.
......@@ -2,10 +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:}{4}{subsubsection.1.2.2}
\contentsline {subsubsection}{\numberline {1.2.3}Data from Legionella pneumophila reference strains:}{11}{subsubsection.1.2.3}
\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}{23}{subsection.3.2}
\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}
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Assembly;Taxonomy;Origin
GCA_001467055.1;Legionella adelaidensis;Burstein
GCA_001467525.1;Legionella anisa;Burstein
GCA_001467505.1;Legionella birminghamensis;Burstein
GCA_001467045.1;Legionella bozemanae;Burstein
GCA_001467025.1;Legionella brunensis;Burstein
GCA_001467035.1;Legionella cherrii;Burstein
GCA_001467545.1;Legionella cincinnatiensis;Burstein
GCA_001467585.1;Legionella drozanskii LLAP-1;Burstein
GCA_001467615.1;Legionella erythra;Burstein
GCA_001467625.1;Legionella feeleii;Burstein
GCA_001467645.1;Legionella geestiana;Burstein
GCA_001467695.1;Legionella gratiana;Burstein
GCA_001467705.1;Legionella hackeliae;Burstein
GCA_001467785.1;Legionella israelensis;Burstein
GCA_001467745.1;Legionella jamestowniensis;Burstein
GCA_001467765.1;Legionella jordanis;Burstein
GCA_001467795.1;Legionella lansingensis;Burstein
GCA_001467825.1;Legionella londiniensis;Burstein
GCA_001467845.1;Legionella maceachernii;Burstein
GCA_001467865.1;Legionella moravica;Burstein
GCA_001467895.1;Legionella nautarum;Burstein
GCA_001467925.1;Legionella oakridgensis;Burstein
GCA_001467945.1;Legionella parisiensis;Burstein
GCA_001467955.1;Legionella quateirensis;Burstein
GCA_001467975.1;Legionella quinlivanii;Burstein
GCA_001468125.1;Legionella rubrilucens;Burstein
GCA_001468105.1;Legionella sainthelensi;Burstein
GCA_001468135.1;Legionella santicrucis;Burstein
GCA_001468025.1;Legionella shakespearei DSM 23087;Burstein
GCA_001468165.1;Legionella spiritensis;Burstein
GCA_001468005.1;Legionella steelei;Burstein
GCA_001468065.1;Legionella steigerwaltii;Burstein
GCA_001468035.1;Legionella tucsonensis;Burstein
GCA_001468085.1;Legionella waltersii;Burstein
GCA_001467535.1;Legionella worsleiensis;Burstein
GCA_900452395.1;Legionella beliardensis;gupta
GCA_002240035.1;Legionella clemsonensis;gupta
GCA_000162755.2;Legionella drancourtii;gupta
GCA_002776555.1;Legionella endosymbiont of Polyplax serrata PsAG;gupta
GCA_000621525.1;Legionella fairfieldensis;gupta
GCA_000953135.1;Legionella fallonii;gupta
GCA_900639875.1;Legionella impletisoli;gupta
GCA_000091785.1;Legionella longbeachae;gupta
GCA_000756815.1;Legionella massiliensis;gupta
GCA_900639915.1;Legionella nagasakiensis;gupta
GCA_000770585.1;Legionella norrlandica;gupta
GCA_900639985.1;Legionella rowbothamii;gupta
GCA_001465875.1;Legionella saoudiensis;gupta
GCA_003070665.1;Legionella taurinensis;gupta
GCA_000308315.1;Legionella tunisiensis;gupta
GCA_000701265.1;Legionella wadsworthii;gupta
GCA_900640115.1;Legionella yabuuchiae;gupta
GCA_001572745.1;Coxiella burnetii;gupta
GCA_000048645.1;Legionella pneumophila Paris;pneumo
GCA_000048665.1;Legionella pneumophila Lens;pneumo
GCA_000008485.1;Legionella pneumophila Philadelphia;pneumo
GCA_000092545.1;Legionella pneumophila Corby;pneumo
GCA_000092625.1;Legionella pneumophila Alcoy;pneumo
GCA_000306865.1;Legionella pneumophila Lorraine;pneumo
GCA_001467875.1;Legionella micdadei;Pillon
GCA_900639865.1;Legionella gresilensis;Pillon
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_001886835.1;Legionella fraseri Dallas1E;Pillon
GCA_003003865.1;Legionella fraseri Lansing 3;Pillon
GCA_003003755.1;Legionella fraseri Los Angeles 1;Pillon
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