Basel phages annotation and clusters

<b>Table (</b><b>Phages_annotation_and_clusters.tsv</b><b>)</b><b>:</b><br>Annotation of Basel phages using current taxonomy information (Family, Subfamily, Genus) extracted from NCBI Taxonomy (version of DATE) and ICTV (sheet 1); The clustering results (sheet 2).<b>Figure (</b><b>heatmap_Phages_clustering.pdf</b><b>)</b><b>:</b><br>Hierarchical clustering of BASEL coliphages using pairwise proteome similarity scores.<br>To cluster the phages on the basis of proteome similarity, the number of shared homologous proteins between all phage pairs were computed and normalised to the phage proteome length, and the matrix of these pairwise similarity scores were used to compute the complement symmetric proteome composition distance (PCD) matrix. Hierarchical clustering using the average-linkage method applied to the PCD matrix was used to generate the dendrogram that determines the phage groupings. Phage annotations followed the latest ICTV update<b>Rscript (</b><b>Cluster_phages_and_get_heatmaps.R):</b><br>Rscript to reproduce phages clustering and visualisation.<br>Input data: i) <b>similarity_scores_matrix.tsv</b>: a matrix with pairwise similarity scores for all phages. ii) <b>s08_descriptions_with_ICTV.tsv</b> an annotation table for the header.<b>表格（Phages_annotation_and_clusters.tsv）</b>：<br>基于NCBI分类学数据库（DATE版本）与国际病毒分类委员会（International Committee on Taxonomy of Viruses, ICTV，sheet 1）提取的最新分类学信息（科、亚科、属），对巴塞尔噬菌体进行注释；聚类结果详见sheet 2。<br><b>图（heatmap_Phages_clustering.pdf）</b>：<br>基于成对蛋白质组相似性得分对巴塞尔大肠杆菌噬菌体进行层级聚类。为依据蛋白质组相似性完成噬菌体聚类，首先计算所有噬菌体对间共享的同源蛋白数量，并将其标准化至噬菌体蛋白质组长度，随后利用该成对相似性得分矩阵计算得到对称互补的蛋白质组组成距离（Proteome Composition Distance, PCD）矩阵。基于PCD矩阵，采用平均连锁法进行层级聚类，生成用于确定噬菌体分组的树状图。噬菌体注释遵循国际病毒分类委员会（ICTV）最新更新版本。<br><b>R脚本（Cluster_phages_and_get_heatmaps.R）</b>：<br>用于复现噬菌体聚类与可视化流程的R脚本。输入数据包括：i) <b>similarity_scores_matrix.tsv</b>：涵盖所有噬菌体的成对相似性得分矩阵；ii) <b>s08_descriptions_with_ICTV.tsv</b>：用于表头注释的注释表。