genes are predicted simultaneously in several aligned genomes
RUNNING AUGUSTUS IN CGP MODE
BUILDING THE NEWICK PARSER FROM SCRATCH
(not needed unless you run into compiler errors related to ‘parse.cc’ or ‘lex.cc’)
AUTHORS AND CONTACT
The cgp mode is an extension to AUGUSTUS that takes an alignment of two or more genomes and simultaneously predicts genes in all of them. Beside the genomes and the alignment, a phylogenetic tree of the species is required input. AUGUSTUS-cgp can either be used
Both genomes and extrinsic evidence can either be read in from a flat file or alternatively retrieved from a MySQL or SQLite database.
All three approaches are described below in more detail.
This manual assumes that you are already familiar with AUGUSTUS and that you know how to use AUGUSTUS for gene prediction in a single genome.
See these instructions for a complete overview.
Open the file common.mk with a text editor and uncomment the following lines to enable comparative gene prediction.
COMPGENEPRED = true
To support a SQLite database uncomment this line
SQLite = true
or for MySQL this
MYSQL = true
Once all dependencies are available, you can compile AUGUSTUS using make.
In case you had previously compiled AUGUSTUS with disabled cgp mode first you have to call
After compilation has finished, the command bin/augustus should be executable and print a usage message.