EMBALMER v0.99.1c

Binaries for Linux, Mac, Windows available.

• "Modern" computers are generally newer than 2011. They should have "AVX." These are the recommended versions (the filenames are uncontaminated with extra stuff).
• "Older" computers are circa 2009 (the very first core-i7's). They should have "SSE4.2."
• "Buzzard" computers are, well... newer than 2006 like the first "cores." They should have "SSSE3."
  Even older computer? The code can compile for any 64-bit processor, but you're on your own (or contact me).

The RefSeq archive is a 16S microbial database for embalmer. EMBALMER also works with plain FASTA files as references. Also included is a taxonomy file for the same RefSeq 16S genes. You should extract the database before using.

To see some of embalmer's new taxonomy interpolation features, you can use the DB and taxonomy file like so on some bacterial 16S reads to align all of the reads to all of their best hits and call full interpolated taxonomy for each:

embalm -r RefSeq_16S.edb -q MY_FASTA_QUERIES.fa -o alignments_and_taxonomy.b6 -f -n -m CAPITALIST -b RefSeq_16S.tax -bs -i 0 -p fast

For a more speculative taxonomy, you can try:

embalm -r RefSeq_16S.edb -q MY_FASTA_QUERIES.fa -o alignments_and_taxonomy.b6 -f -n -m CAPITALIST -b RefSeq_16S.tax -bc 3 -i 0 -p fast