
MOCAT v2.0 has a few major changes comapred to MOCAT v 1.x.
Here a few are highlighted:

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MOCAT 1 used the options -only_map, -no_screened_files, -no_extracted_files
MOCAT 2 uses -screened_files, and -extracted_files, and if non are specified,
this is equivalent of specifying -only_map in MOCAT v 1.x.
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MOCAT 2 uses the option -mode NCBI, rather than -mode RefMG as in MOCAT v 1.x.
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MOCAT 2 ships with an updated version of the RefMG.v1 map file. Taxa annotated
as 'undef' in MOCAT v 1.x will be annotated as 'unclassified X' where X is the
cloest lower rank name.
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When profiling, MOCAT 1 produced many output files, MOCAT 2 saves them all in a single
.zip file for each samples, and for the 'pasted profiles', a single .zip file
for the final profile tables
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