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Software and Datasets Developed in the Lab (still being updated)
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Automated genome annotation pipeline that includes self-training, RNAseq incorporation in training and prediction, functional annotation, and comparative genomics. Developed by Jon Palmer with input from Jason Stajich
Automated genome assembly for simple genome projects (best for Haploids)
Genomics Tools
Automated genome annotation pipeline that includes self-training, RNAseq incorporation in training and prediction, functional annotation, and comparative genomics. Developed by Jon Palmer with input from Jason Stajich
Automated genome assembly for simple genome projects (best for Haploids)
Low/Medium Coverage Zygo Genome assembly and annotation
Tools for calculating summary statistics for public fungal genomes in NCBI and downloading genomes and annotations
Protein HMMs for several public phylogenomic marker sets for Fungal Phylogenomics
An alternate tool for genome completeness that incorporates coding and non-coding elements
Transposable element insertion site mapping tool using short-reads for population resequencing
Datasets
Automated genome annotation pipeline that includes self-training, RNAseq incorporation in training and prediction, functional annotation, and comparative genomics. Developed by Jon Palmer with input from Jason Stajich
Automated genome assembly for simple genome projects (best for Haploids)
Low/Medium Coverage Zygo Genome assembly and annotation
Tools for calculating summary statistics for public fungal genomes in NCBI and downloading genomes and annotations
Protein HMMs for several public phylogenomic marker sets for Fungal Phylogenomics
An alternate tool for genome completeness that incorporates coding and non-coding elements
Transposable element insertion site mapping tool using short-reads for population resequencing