Tools

Our approach to software development has been to build tools that we and our collaborators need in our bioinformatic workflows. We hope that some of these tools are useful to others and are always looking for feedback and suggestions for improvement!

AnnoTree

Visualization of genomic annotations across the tree of life

 AnnoView (beta)

Exploration of gene neighborhoods across the tree of life

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PhyloCorrelate

Statistical detection of co-occurring genes across phylogenetic trees

 DiffBase

A bioinformatic database and phylogenetic classification of C. difficile toxins

 PathFams

A database of pathogen-associated protein domains, and additional statistics on PFAM families.

 AXIOME3 (Neufeld Lab)

Automated QIIME 2 Workflow wrapped in Luigi Framework

 MetAnnotate

Function-specific taxonomic profiling of metagenomes.