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Announcements
- February 25-28, 2018
European Conference on Fungal Genetics, Haifa, Israel - March 13-16, 2018
Fungal genomics workshop @ JGI User Meeting, San Francisco, CA, U.S.A. - July 16-21, 2018
International Mycological Society Annual Meeting, San Juan, Puerto Rico
Releases
- March 7, 2024
Aspergillus fumigatus P4 SB v1.0 - March 7, 2024
Penicillium ribium P3 SB v1.0 - January 30, 2024
Trebouxiophyceae sp. bin 3300059473_978 v1.0 - January 30, 2024
Trebouxiophyceae sp. bin 3300059473_6682 v1.0 - January 30, 2024
Chlorellaceae sp. bin 3300059473_4402 v1.0
Credits
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.