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MEGAN2 will be released later this year (August 2007?)

This version will have many new features, including:

- command line mode for non-interactive processing of data
- multi-window capability for multiple analyses simultaneously
- a comparsion mode that can be used to display multiple datasets in
one tree (using pie charts at nodes to show the relative numbers of reads
from the different datasets)
- an extractor mode for extracting all reads from a FastA file that
are mapped to a given taxon
- enhanced taxon identification using GI, EMBL and other accession numbers
- a new algorithm for assigning reads to taxa that uses a 90% rule
- the capability of disabling taxa in the analysis
- a new COG window that shows the number of different COGs found in
the data sets
- a new charts window that can be used to generate heatmaps, pie
charts and histograms for single and multi-data comparisons, both for
taxa and COGs
- a retention index computation that produces a plot that shows how
fast the number of identified species is growing with the number of

Most of these features are already implemented and we are currently in
the testing and debugging stage.
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