Stajich Laboratory for Fungal Evolutionary Genomics

Tools

Links to Projects and Software written or contributed to by the lab.

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 Assembly For The Fungi - automated genome assembly for simple haploid genome projects

Phylogenomic package

More

BioPerl project code

Standard Operating Procedures for Data analyses

ZyGoLife - Low Coverage Genome assembly and annotation

Zygomycetes Genealoogy of Life

1kFG project

calculating summary statistics for public fungal genomes in NCBI and downloading genomes and annotations

downloads and processing for 1kfg project datasets from JGI and other

HMMs for several public phylogenomic marker sets for Fungal Phylogenomics

Fungal Genome Mapping Pipeline - 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