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- BioStar 1537 days ago
- Set up the environment
bash source /path/to/install/mugsyenv.sh
- Run mugsy
mugsy --directory /data/output --prefix mygenomes genome1.fasta genome2.fasta genome3.fasta
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.- View or parse MAF output
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.java -jar gmaj.jar mygenomes.maf
- Set up the environment
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