Table 1. Comparison of aligner features.

A checkmark means the feature is present and usable, otherwise the feature is absent or its use is impractical. Features that are absent by design are marked with a dash.

Aligner	Graphical User Interface	Multi-platform Windows/Linux	Multi-threaded	Callable from C++, scripting languages	Whole genome aln.	Short read aln.	Long read aln.	SAM format output	P-value output
MUMmer4			✔	✔	✔	✔	✔	✔
MUMmer3					✔
Blast	✔	✔	✔		✔				✔
Blat					✔				✔
Mauve	✔	✔			✔
LASTZ					✔			✔	✔
bwa-mem			✔		-	✔	✔	✔
Bowtie2			✔		-	✔	-	✔
BLASR			✔		-	-	✔	✔	✔