CloVR-Comparative supports comparative microbial genome analysis based on reference-free whole-genome alignments and includes the following features that have become community-accepted standard components in most microbial genomics projects:

  1. Identification of unique, shared and core genome fragments, genes and single nucleotide polymorphisms (SNPs).
  2. Prediction of phylogenetic relationships.
  3. Web-based browsing capabilities of comparative genome analysis results.
  4. Visualization of comparative genome analysis results and summary reporting.

CloVR-Comparative accepts as an input two or more annotated genomes in Genbank format that are uploaded by the user (multiple files can be uploaded at once as a compressed archive), a list of Genbank accessions, and/or RefSeq genomes selected via the CloVR comparative pipeline wizard. Genomes to be analyzed can be a combination of finished gap-free and/or draft genomes.

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CloVR-Comparative generates several output files including a summary report with references for the main tools used, circular plots showing comparative analysis results for each input genome, phylogenetic tree figures and a newick/tree format file for downstream processing, detailed analysis result reports for each input genome, clusters of syntenic orthologs, a multiple whole genome alignment file in MAF format, a table of SNPs detected across the aligned genomes, and an interactive Sybil website for future analyses.