Genome Clusters

Click here to access the tool for getting clusters of similar genomes as defined at different GSS or DNA signature thresholds.

Citation: Moreno-Hagelsieb G, Wang Z, Walsh S, ElSherbiny A (2013) Phylogenomic clustering for selecting non-redundant genomes for comparative genomics. Bioinformatics 29 (7): 947-949..

Find here data regarding genomic similarity scores (GSS) and their use for reducing the set of genomes in our database into a non-redundant set for comparative genomics, or for whatever else you might want to do with each group or cluster of similar genomes. The measure for similarity is explained in several articles by members of our group. We also provide distances between genomes based on di-, tri- and tetra-nucleotide signatures. The R scripts require three libraries: cluster, MCMCpack and ape. The scripts will produce groups of redundant genomes, transform the score tables into matrices, and provide dendogram files in Newick format (common format for phylogenetic trees).

  • Click here to access the tool for getting clusters of similar genomes as defined at different GSS or DNA signature thresholds.
  • Click here to get the file containing all-against-all GSS as used in the article and in the R-script provided below.
  • Click here for the R-script used to cluster the genomes using the GSS from the file above.
  • Divisive clusters in Newick format can be accessed here for GSSa, GSSb and GSSc.
  • To get the files containing all-against-all DNA signatures as used in the article and in the R-scripts provided below, click here: di-nucleotide, tri-nucleotide and tetra-nucleotide.
  • For the R-scripts used to cluster the genomes using the DNA signatures from the files above: di-nucleotide, tri-nucleotide and tetra-nucleotide.
  • Divisive clusters in Newick format can be accessed here for di-nucleotide, tri-nucleotide and tetra-nucleotide signatures.
  • Click here for a table with further information about the genomes in the current release (NCBI accessions and such). A tab-separated text version is also available.
  1. February 10th, 2013
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