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Circos banding/histograms/scatterplots
Circos synteny bands
opscan ortholog finder
mummer4
Alignment --
BWA
Gsnap
Gmap
Blasr
Hisat2
redtandem tandem duplication software
repeatmodeler
repeatmasker
repeatexplorer
LTR finder
inverted repeat finder
Helitron scanner
Meme to fimo
Blobtools
GATK
GeneOverlap R package
Busco
Pyscaf
Falcon assembly
Multiple Alignment --
muscle
clustalw
Phylogenetic tree --