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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