HI Mothur group,
I am trying unifrac distance on my data and then testing with Amova
mothur “#unifrac.unweighted(tree=test.phylip.tre, group=file.subsample.groups,iters=10000,distance=lt)”
mothur “#amova(phylip=est.subsample.phylip.tre1.unweighted.phylip.dist, design=Group_mothur.design)”
but its not giving me proper comparisons. I mean I have 4 groups and in my design file,something like this below
out is like this
1KO_CH-2KO_SH-3WT_CH-4WT_CH Among Within Total
SS 1.08993 10.6001 11.6901
df 3 30 33
MS 0.363309 0.353338
Amova test is giving combined group comparison pvalue but i want pairwise comparison for each group.
Is there any other command with is alternative or i have done some mistake?