CodingQuarry   Gene prediction software optimised for gene-dense genomes such as those of Fungi.   (A. Testa)

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts
AC Testa, JK Hane, SR Ellwood, RP Oliver
BMC Genomics 16 (1), 170 (2015)

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RIPCAL/deRIP   Calculate repeat-induced point mutation in fungal genomes (J. Hane)

RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences
J Hane, R Oliver
BMC bioinformatics 9 (1), 478 (2008)

In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes
J Hane, R Oliver
BMC genomics 11 (1), 655 (2010)

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CDSMapper   Collection of proteogenomics scripts for mapping peptides to genomic coordinates, testing for potential UTR boundary and frameshift errors (J. Hane)

Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum
S Bringans, J Hane, T Casey, KC Tan, R Lipscombe, P Solomon, R Oliver
BMC bioinformatics 10 (1), 301

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Coming Soon:

OcculterCut   Segment genomes into regions of consistent G:C content.  Identify bi-modal G:C biases.  Report genes within or proximal to A:T-rich regions.  (A. Testa)