Change rarefaction to work with BIOM HDF5
Use BIOM HDF5 with beta diversity
Use write_biom_table in compute_core_microbiome
Change alpha_diversity to use write_biom_table
Remove test of format_biom_table

The function being tested was removed
Change test_make_otu_network: use write_biom_table

also reformat the call to the Table constructor
Use latest BIOM API in qiime/make_otu_network
Remove unused import of format_biom_table
Merge pull request #18 from adamrp/compute_core_microbiome

Compute core microbiome
use biom_open
Merge pull request #16 from adamrp/rarefaction

Rarefaction
Merge pull request #17 from adamrp/beta_diversity

Beta diversity
Merge pull request #21 from adamrp/test_format

Test format
Merge pull request #25 from adamrp/summarize_otu_by_cat

Summarize otu by cat
Merge pull request #23 from adamrp/test_otu_significance

Test otu significance
Merge pull request #22 from adamrp/test_make_otu_network

Test make otu network
Merge pull request #20 from adamrp/alpha_diversity

Alpha diversity
use biom_open with split_otu_table_by_taxonomy
use biom_open with sort_otu_table
API: Use HDF5 in filter_distance_matrix.py

I've also made a few cosmetic changes :lipstick: