This is alpha-quality software.

Pairwise alignments of coding sequences, using a modification of the algorithm described in the MACSE paper:

V. Ranwez, S. Harispe, F. Delsuc, and E. J. P. Douzery “MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.” PloS one, vol. 6, no. 9, p. e22594, Jan. 2011.

Requires cmake, libz-dev, and a compiler supporting C++11 (tested on g++ 4.6.3, clang++ 3.2).

To build:

make

The resulting executable will be placed in _build/Release/codon-sw

codon-sw <ref.fasta> <query.fastq> <output_bam>

Generates:

• <output_bam> - BAM-format alignments to ref.fasta

If a --fasta-pairs option is provided, pairwise codon-alignments (which may be directly translated) are written to the argument.

To modify scoring parameters, see options in codon-sw -h.

BSD 3-clause.

The excellent SeqAn library is bundled with the source in the deps/seqan subdirectory. See deps/seqan/LICENSE for license information.