Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.
To cite Mugsy, use:
Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes.Bioinformatics 2011 27(3):334-4
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This example will align three genomes and output a file /data/output/mygenomes.maf. The --directory setting is also used for storing temporary files during the run.
The prefix of each input filename will be used as the genome name in the output files (eg. genome1 from genome1.fsa). Header lines in the FASTA files should not contain ':' or '-' to avoid parsing problems.
The output of Mugsy is Multiple Alignment Format (MAF).
One option for browsing is GMAJ, which provides a reference-based stand-alone viewer for MAF files.