- added min_alignment_len option to filter out short alignments in local mode. For long reads (>150) it is now recommended to use local mapping together with "--min_alignment_len 100" to filter out very short alignments. (by Tin)
- added "--samout" option to store the mapping file in SAM format (the SAM will be compressed if the extension of the specified output file ends with ".bz2") (by Tin)
- fix: MetaPhlAn2 now ingores about ~300 markers that were a-specific (thanks to Eric)