deletions | additions       diff --git a/Materials and Methods.tex b/Materials and Methods.tex  index b229ebe..836dfa6 100644  --- a/Materials and Methods.tex  +++ b/Materials and Methods.tex 
...
To perform a phylogenetic analysis of Yersinia species, 16S ribosomal subunit sequence was downloaded from GenBank. In total 34 RefSeq sequences from 17 different Yersinia species were analysed (Table 1). To supplement the analysis with \textit{Y.enterocolitica} species from the full spectrum of biovars (1A, 1B and 2-5), contigs from fifteen \textit{Y.enterocolitica} samples, reported in Reuter et al, were downloaded from the European Nucleotide Archieve \cite{24753568} (Table 2). Where not already available, 16S ribosomal subunit nucleotide sequence were extracted from assembled contigs using the RNAmmer server (v1.2) \cite{17452365}. 16S FASTA sequences were aligned using Clustal Omega \cite{21988835}\cite{20439314}\cite{23671338} and alignment files were used to construct phylogenetic trees in Seaview using a parsimony model with 100 bootstrap replicates \cite{19854763}.  Contigs were scaffolded to a reference Y.enterocolitica genome (Genbank: AM286415.1) using the Contiguator web application (http://combo.dbe.unifi.it/contiguator) \cite{21693004}. Scaffold and contig assemblies were annotated with gene features using two independent tools; PROKKA \cite{24642063} and the RAST server \cite{18261238}\cite{24293654}. \cite{18261238,24293654}.  Annotations is Genbank format were uploaded to Artemis for visulaisation \cite{11120685}. PathogenFinder v1.1 and ResFinder v2.1 were used to identify and rank pathogenic genes and antibiotic resistance genes respectively \cite{24204795} \cite{22782487}. The identification of bacterial insertion sequences was performed using the ISFinder website (https://www-is.biotoul.fr/) \cite{16381877}.