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 eShadow 

Evolutionary phylogenetic SHADOWing of closely related species
http://eshadow.dcode.org/

I. Ovcharenko, D. Boffelli, and G. Loots, eShadow: A Tool for Comparing Closely Related Sequences, Genome Research, 14(6), 1191-1198 (2004)

Example multiple sequences/alignments:
APOB exon: sequences visualization 2 distant species mouse
PLG exon: sequences visualization 2 distant species mouse
2 exons of LXRalpha: trimmed sequences  visualization 2 distant species mouse
CETP exon: sequences visualization 2 distant species

Phylodendron - Phylogenetic tree printer

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