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Fungal genome analysis pipelines and analysis systems are using a number of software tools and databases. Their availability and value is gratefully acknowledged:

  1. RepeatMasker - masking DNA sequences for interspersed repeats and low complexity DNA sequences
  2. RepeatScout - de novo repeat family identification
  3. BLAST - sequence similarity searches
  4. BLAT - sequence similarity searches
  5. tRNAScan - tRNA prediction
  6. RNAmmer - rRNA prediction
  7. Infernal - for RNA structures and sequences
  8. RNAz - search for RNA secondary structures in multiple sequence alignments
  9. Fgenesh - eukaryotic gene predictors (combination of tools)
  10. Wise - homology-based gene prediction
  11. GeneMark-ES - ab initio gene predictor for fungal genomes
  12. InterProScan - InterPro annotation
  13. SignalP - signal peptide annotations.
  14. TMHMM - transmembrane helices annotation.
  15. TimeLogic DeCypher - hardware accelerated sequence alignments and domain predictions
  16. MCL - clustering protein sequences.
  17. MAFFT - multiple sequence alignment for gene tree building.
  18. RAxML - Maximum-likelihood phylogeny estimation.
  19. Gblocks - filtering sequence alignments
  20. Notung - Gene and species tree reconciliation
  21. CLUSTALW - multiple sequence alignment.
  22. VISTA - whole-genome alignments for synteny analysis.