Amova test

Commands in mothur
1

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 “#pcoa(phylip=test.subsample.phylip.tre1.unweighted.phylip.dist)”
and then
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
S01 1KO_CH
S02 1KO_CH
S03 1KO_CH
S04 1KO_CH
S05 2KO_SH
S06 2KO_SH
S07 2KO_SH
S08 2KO_SH
S09 3WT_CH
S10 3WT_CH
S11 3WT_CH
S12 3WT_CH
S13 4WT_CH
S14 4WT_CH
S15 4WT_CH

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

Fs: 1.02822
p-value: 0.258

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?

2

It is because the p-value for the test that one of the four groups is different from the others is 0.258. Since there aren’t any groups that are significantly different from the others it does not move on to the pairwise comparisons.

Pat