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Announcements
- August 10-14, 2013
MycoCosm workshop @ APS-MSA Joint Meeting, Austin, TX, U.S.A. - March 26-28, 2013
JGI User Meeting, Walnut Creek, CA, USA - March 12-17, 2013
Fungal Genetics Meeting in Asilomar, Pacific Grove, CA, USA - January 12-16, 2013
Plant and Animal Genomics Meeting, San Diego, CA, USA
Releases
- June 3, 2013
Aureobasidium pullulans var. melanogenum v1.0 - June 3, 2013
Aureobasidium pullulans var. namibiae v1.0 - May 31, 2013
Cylindrobasidium torrendii v1.0 - May 31, 2013
Melanomma pulvis-pyrius v1.0 - May 23, 2013
Aulographum hederae v2.0
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.
