ubuntu2404
\relax
\providecommand \babel@aux [2]{\global \let \babel@toc \@gobbletwo }
\@nameuse{bbl@beforestart}
\bibstyle{biblatex}
\bibdata{main-blx,references}
\citation{biblatex-control}
\abx@aux@refcontext{none/global//global/global/global}
\providecommand\hyper@newdestlabel[2]{}
\providecommand\HyField@AuxAddToFields[1]{}
\providecommand\HyField@AuxAddToCoFields[2]{}
\citation{blattner1997complete}
\abx@aux@cite{0}{blattner1997complete}
\abx@aux@segm{0}{0}{blattner1997complete}
\citation{tenaillon2010genome}
\abx@aux@cite{0}{tenaillon2010genome}
\abx@aux@segm{0}{0}{tenaillon2010genome}
\providecommand \oddpage@label [2]{}
\babel@aux{english}{}
\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{1}{section.1}\protected@file@percent }
\newlabel{sec:introduction}{{1}{1}{Introduction}{section.1}{}}
\newlabel{sec:introduction@cref}{{[section][1][]1}{[1][1][]1}{}{}{}}
\@writefile{toc}{\contentsline {section}{\numberline {2}Materials and Methods}{2}{section.2}\protected@file@percent }
\newlabel{sec:methods}{{2}{2}{Materials and Methods}{section.2}{}}
\newlabel{sec:methods@cref}{{[section][2][]2}{[1][1][]2}{}{}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Genomic Data Acquisition and Processing}{2}{subsection.2.1}\protected@file@percent }
\@writefile{toc}{\contentsline {subsection}{\numberline {2.2}Sequence Alignment and Distance Calculation}{2}{subsection.2.2}\protected@file@percent }
\@writefile{toc}{\contentsline {subsection}{\numberline {2.3}Phylogenetic Analysis}{2}{subsection.2.3}\protected@file@percent }
\@writefile{toc}{\contentsline {section}{\numberline {3}Results}{2}{section.3}\protected@file@percent }
\newlabel{sec:results}{{3}{2}{Results}{section.3}{}}
\newlabel{sec:results@cref}{{[section][3][]3}{[1][2][]2}{}{}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Genomic Sequence Composition Analysis}{2}{subsection.3.1}\protected@file@percent }
\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Comprehensive genomic sequence composition analysis of \textit {E. coli} strains. (Top left) GC content distribution showing the typical range for \textit {E. coli} genomes. (Top right) Nucleotide count heatmap revealing strain-specific composition patterns. (Bottom left) GC vs AT content relationship demonstrating complementary base pairing constraints. (Bottom right) Genomic diversity index based on cumulative evolutionary distances, highlighting the most divergent strains.}}{3}{figure.caption.1}\protected@file@percent }
\providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
\newlabel{fig:sequence_composition}{{1}{3}{Comprehensive genomic sequence composition analysis of \species {E. coli} strains. (Top left) GC content distribution showing the typical range for \species {E. coli} genomes. (Top right) Nucleotide count heatmap revealing strain-specific composition patterns. (Bottom left) GC vs AT content relationship demonstrating complementary base pairing constraints. (Bottom right) Genomic diversity index based on cumulative evolutionary distances, highlighting the most divergent strains}{figure.caption.1}{}}
\newlabel{fig:sequence_composition@cref}{{[figure][1][]1}{[1][2][]3}{}{}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Phylogenetic Relationships and Evolutionary Distances}{3}{subsection.3.2}\protected@file@percent }
\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Phylogenetic analysis of \textit {E. coli} strain relationships using distance-based methods. (Top left) UPGMA phylogenetic tree showing evolutionary relationships and clustering patterns. (Top right) Symmetric distance matrix heatmap revealing pairwise evolutionary distances. (Bottom left) Horizontal dendrogram view for detailed examination of clustering hierarchy. (Bottom right) Distribution of pairwise evolutionary distances with statistical measures.}}{4}{figure.caption.2}\protected@file@percent }
\newlabel{fig:phylogenetic_analysis}{{2}{4}{Phylogenetic analysis of \species {E. coli} strain relationships using distance-based methods. (Top left) UPGMA phylogenetic tree showing evolutionary relationships and clustering patterns. (Top right) Symmetric distance matrix heatmap revealing pairwise evolutionary distances. (Bottom left) Horizontal dendrogram view for detailed examination of clustering hierarchy. (Bottom right) Distribution of pairwise evolutionary distances with statistical measures}{figure.caption.2}{}}
\newlabel{fig:phylogenetic_analysis@cref}{{[figure][2][]2}{[1][3][]4}{}{}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.3}Comparative Genomics and Functional Analysis}{4}{subsection.3.3}\protected@file@percent }
\citation{touchon2009organised}
\abx@aux@cite{0}{touchon2009organised}
\abx@aux@segm{0}{0}{touchon2009organised}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.4}Gene Content and Functional Diversity Visualization}{5}{subsection.3.4}\protected@file@percent }
\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces Gene content and functional diversity analysis across \textit {E. coli} strains. (Top left) Gene family presence/absence heatmap showing strain-specific gene content patterns. (Top right) Conservation scores for different gene families, with core metabolic functions showing highest conservation. (Bottom left) Gene family diversity by strain, indicating variable gene content across strains. (Bottom right) Gene content-based clustering using Jaccard distances, revealing functional similarity patterns independent of phylogenetic relationships.}}{5}{figure.caption.3}\protected@file@percent }
\newlabel{fig:gene_content_analysis}{{3}{5}{Gene content and functional diversity analysis across \species {E. coli} strains. (Top left) Gene family presence/absence heatmap showing strain-specific gene content patterns. (Top right) Conservation scores for different gene families, with core metabolic functions showing highest conservation. (Bottom left) Gene family diversity by strain, indicating variable gene content across strains. (Bottom right) Gene content-based clustering using Jaccard distances, revealing functional similarity patterns independent of phylogenetic relationships}{figure.caption.3}{}}
\newlabel{fig:gene_content_analysis@cref}{{[figure][3][]3}{[1][4][]5}{}{}{}}
\@writefile{toc}{\contentsline {section}{\numberline {4}Discussion}{5}{section.4}\protected@file@percent }
\newlabel{sec:discussion}{{4}{5}{Discussion}{section.4}{}}
\newlabel{sec:discussion@cref}{{[section][4][]4}{[1][5][]5}{}{}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}Genomic Diversity and Evolutionary Patterns}{5}{subsection.4.1}\protected@file@percent }
\@writefile{toc}{\contentsline {subsection}{\numberline {4.2}Gene Content Variation and Functional Implications}{5}{subsection.4.2}\protected@file@percent }
\@writefile{toc}{\contentsline {subsection}{\numberline {4.3}Methodological Considerations and CoCalc Integration}{6}{subsection.4.3}\protected@file@percent }
\@writefile{toc}{\contentsline {subsection}{\numberline {4.4}Future Directions and Extensions}{6}{subsection.4.4}\protected@file@percent }
\@writefile{toc}{\contentsline {section}{\numberline {5}Conclusions}{6}{section.5}\protected@file@percent }
\newlabel{sec:conclusions}{{5}{6}{Conclusions}{section.5}{}}
\newlabel{sec:conclusions@cref}{{[section][5][]5}{[1][6][]6}{}{}{}}
\abx@aux@read@bbl@mdfivesum{F7D18C6A17CD6349EFF8FD341445FFBD}
\abx@aux@defaultrefcontext{0}{blattner1997complete}{none/global//global/global/global}
\abx@aux@defaultrefcontext{0}{tenaillon2010genome}{none/global//global/global/global}
\abx@aux@defaultrefcontext{0}{touchon2009organised}{none/global//global/global/global}
\abx@aux@defaultlabelprefix{0}{blattner1997complete}{}
\abx@aux@defaultlabelprefix{0}{tenaillon2010genome}{}
\abx@aux@defaultlabelprefix{0}{touchon2009organised}{}
\gdef \@abspage@last{7}