Fungal genome analysis pipelines and analysis systems are using a number of software tools and databases. Their availability and value is gratefully acknowledged:
- RepeatMasker - masking DNA sequences for interspersed repeats and low complexity DNA sequences
- RepeatScout - de novo repeat family identification
- BLAST - sequence similarity searches
- BLAT - sequence similarity searches
- tRNAScan - tRNA prediction
- RNAmmer - rRNA prediction
- Infernal - for RNA structures and sequences
- RNAz - search for RNA secondary structures in multiple sequence alignments
- Fgenesh - eukaryotic gene predictors (combination of tools)
- Wise - homology-based gene prediction
- GeneMark-ES - ab initio gene predictor for fungal genomes
- InterProScan - InterPro annotation
- SignalP - signal peptide annotations.
- TMHMM - transmembrane helices annotation.
- TimeLogic DeCypher - hardware accelerated sequence alignments and domain predictions
- MCL - clustering protein sequences.
- MAFFT - multiple sequence alignment for gene tree building.
- RAxML - Maximum-likelihood phylogeny estimation.
- Gblocks - filtering sequence alignments
- Notung - Gene and species tree reconciliation
- CLUSTALW - multiple sequence alignment.
- VISTA - whole-genome alignments for synteny analysis.