Distance Types

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Martin Vickers edited this page Oct 11, 2018 · 33 revisions

d2

d2s

d2star

D2S

To select D2S as a distance measurement within KAST, use the -t D2S flag.

$D_{2}^{S}(\widetilde{C}_{X},\widetilde{C}_{Y})=\sum_{i=1}^{4^{k}}\frac{\widetilde{C}_{X},i\widetilde{C}_{Y},i}{\sqrt{\widetilde{C}_{X}^{2},i+\widetilde{C}_{Y}^{2},i}}$

Reinert G, Chew D, Sun F (2009) Waterman MS: Alignment-free sequence comparison (I): statistics and power. J Comput Biol 12: 1615–1634.

D2Star (AKA D2*)

To select D2Star as a distance measurement within KAST, use the -t D2Star flag.

$D_{2}^{*}(\widetilde{C}_{X},\widetilde{C}_{Y})=\sum_{i=1}^{4^{k}}\frac{\widetilde{C}_{X},i \widetilde{C}_{Y},i}{\sqrt{\sqrt{n_{X}P_{X},i}\sqrt{n_{Y}P_{Y},i}}}$

Reinert G, Chew D, Sun F (2009) Waterman MS: Alignment-free sequence comparison (I): statistics and power. J Comput Biol 12: 1615–1634.

NGD

bc

DAI

Manhattan

Chebyshev