Clustering of samples based on tetra nucleotide frequency

[chayan]

Hi All,

I have assembled several metagenomic samples of various sequencing depth. The contigs have been annotated with COG. Now I want to cluster them based on tetra nucleotide frequency and COG categories.

any suggestions??

thanks
chayan

[TiborNagy]

The frequency of every kmer should be a dimension. Than you can use PCA.

[chayan]

The frequency of every kmer should be a dimension. Than you can use PCA.

Thanks i did it already but additionaly i want to cluster my samples based on the frequency of cog categories and finaly plot in NMDS (nonmetris mds), as i am not well aware of this so now i am looking for a suitable package