Distance Types

Here you will find complete descriptions of all the alignment-free distance measures implemented with KAST along with references.

d2

To select d2 as a distance measurement within KAST, use the -t d2 flag.

d2s

To select d2 as a distance measurement within KAST, use the -t d2s flag.

Wang Y, Liu L, Chen L, Chen T, Sun F. Comparison of Metatranscriptomic Samples Based on k-Tuple Frequencies. Parkinson J, ed. PLoS ONE. 2014;9(1):e84348. doi:10.1371/journal.pone.0084348.

d2star (AKA d2*)

To select d2 as a distance measurement within KAST, use the -t d2star flag.

Wang Y, Liu L, Chen L, Chen T, Sun F. Comparison of Metatranscriptomic Samples Based on k-Tuple Frequencies. Parkinson J, ed. PLoS ONE. 2014;9(1):e84348. doi:10.1371/journal.pone.0084348.

D2S

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

Reinert G, Chew D, Sun F, Waterman MS. Alignment-Free Sequence Comparison (I): Statistics and Power. Journal of Computational Biology. 2009;16(12):1615-1634. doi:10.1089/cmb.2009.0198.

D2Star (AKA D2*)

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

Reinert G, Chew D, Sun F, Waterman MS. Alignment-Free Sequence Comparison (I): Statistics and Power. Journal of Computational Biology. 2009;16(12):1615-1634. doi:10.1089/cmb.2009.0198.

NGD

Bray-Curtis

DAI

Euler

Manhattan

Chebyshev