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AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
To run this software interactively in a Linux environment run the commands:
module load augustus augustus [parameters] --species=SPECIES queryfilename
Augustus requires 2 arguments: the species name and a queryfile containing the input sequence in FASTA format. To view a list of available species, use the command:
A description of parameters and more information can be found on the Augustus homepage.