Function：
Non-metric multidimensional scaling (NMDS) is a rank-based and indirect gradient analysis approach which produces an ordination based on a distance or dissimilarity matrix.

Input：

（1） The input file can be abundance table(OTU,species,funtion abundance table)or similarity distance matrix

（2）Grouping file is optional. The tool supports no more than 2 grouping information in a single sample.

（3） The input file should be a tab-delimited “.txt” file

Parameters：

（1）Dot size：Dot size: define the dots size（the default value is 3）

（2）Group name：define the group name

（3）Dot transparency：define the dots transparency if case of overlapping of dots

Output：

nmds_sites.xls：document dot sites in an NMDS plot.

nmds_plot.pdf/png: NMDS_plot.png/pdf: NMDS plot of NMDS1-NMDS2, NMDS1-NMDS3 and NMDS2-NMDS3.

Tool machinery：

(1)If importing an OTU table, the tool will first normalize each OTU in the relative abundance, then calculate sample similarity distance of Bray-Curtis by R. Finally, PCoA is performed in R and plotted using ggplot2 software.

(2)If importing similarity distance matrix (e.g. Unifrac distance), the PCoA tool will calculate and plot a chart directly from the input matrix.