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Table 1 Overview of tools for visualising alignments

From: Alvis: a tool for contig and read ALignment VISualisation and chimera detection

  Genome alignment Read alignment Input formats Interactive viewer Output formats Platforms supported
Alvis Yes Yes BLAST, MUMmer, SAM, PAF, PSL No TeX(PDF), SVG Java (Linux, Mac, Windows)
Artemis Yes Yes BAM Yes Java 9 only
BLAST Web No Yes No Webpage Browser based
Circos Yes Yes Bespoke format No PNG, SVG Linux, Mac, Windows
Icarus Yes No Yes Linux, Mac
Mauve Yes No Yes PDF Linux, Mac, Windows
MUMmerplot Yes No MUMmer No Postscript, X11 Linux, Mac
  1. The Input Formats field is left empty when the visualisation is part of an alignment pipeline. The Output Formats field is left empty if the visualisation appears in an interactive display