Let's say, I have sequence data of bacterial communities from multiple samples, I want to find out what bacteria are either negatively or positively associate with other bacteria. What software or tools can I use to do this analysis?
SparCC is set up to do just this.
See:
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002687
Is it 16S or shotgun sequencing? If 16S, Mothur. If shotgun, then Ray Meta if you have good computer ressources (http://genomebiology.com/2012/13/12/R122). If not you could try MetaPhyler, which gives pretty good profiling results qui fast (http://metaphyler.cbcb.umd.edu/). If you're not good with computers, try MG-RAST, but it may take a while before you get your results (http://metagenomics.anl.gov/).
Frederic Raymond: It worked well for me! Paper coming out soon in Molecular Ecology.
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