Evan Kiefl of anvi'o


Computational biologist and software developer. For my PhD I studied how selective pressures shape the evolution of proteins in naturally occurring microbial populations.


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Intellectual contributions

Some contributions are more than code. Inevitably, this manually curated list will be incomplete for almost everyone, but nevertheless, we try to keep track of key contributions made by memebers of the anvi'o commmunity to the platform and its users. Edit these files to help.

  • Spearheaded the development of protein structure prediction, analysis, and visualization capabilities within anvi'o.
  • Redesigned mission-critical code related to metagenomic workflows, decreasing compute times from >100 hours to <1 hour for terabyte-scale analyses.
  • Made significant contributions to the overall health and maintenance of the codebase through code reviews, performance refactoring, feature implementation, and issue diagnosis.
  • Made significant contributions to the storage, processing, and analysis strategies related to single nucleotide variants (SNVs), single codon variants (SCVs), single amino acid variants (SAAVs), and insertions/deletions (INDELs).
  • Made significant contributions to documentation, totaling >3,000 lines of codebase documentation and >20,000 words of blogs/tutorials/workflows.

Program contributions

anvi-compute-genome-similarity anvi-db-info anvi-delete-misc-data anvi-dereplicate-genomes anvi-display-structure anvi-export-gene-calls anvi-export-locus anvi-export-misc-data anvi-export-structures anvi-gen-contigs-database anvi-gen-fixation-index-matrix anvi-gen-structure-database anvi-gen-variability-profile anvi-get-pn-ps-ratio anvi-get-short-reads-from-bam anvi-import-misc-data anvi-init-bam anvi-migrate anvi-profile anvi-report-inversions anvi-run-hmms anvi-run-interacdome anvi-search-palindromes anvi-setup-interacdome anvi-setup-pdb-database anvi-show-misc-data anvi-update-structure-database anvi-script-filter-fasta-by-blast anvi-script-gen-pseudo-paired-reads-from-fastq anvi-script-get-coverage-from-bam anvi-script-reformat-fasta

Resource contributions

Tutorials and exercises

Kinds of write-ups that typically use mock or simple datasets to describe basic concepts and how to accomplish common tasks in anvi'o often with hands-on experience.

Anvi'o tools for microbial population genetics A theoretical tutorial describing how to characterize SNVs, SCVs and SAAVs with anvi’o, and how to interpret the output.
A primer on anvi'o with the Infant Gut Dataset A tutorial that walks you through some of the most fundamental aspects of anvi'o and its application to a real-world dataset organized in multiple interconnected chapters, which all use the same dataset.

Technical write-ups

Solutions or discussions regarding matters that are typically more technical than scientific.

Extract loci from genomes and metagenomes with anvi'o A tutorial on how to use anvi-export-locus to target genomic regions of interest across genomes and/or metagenomic assemblies, and report sequences and/or anvi’o contigs databases for cut loci for downstream analyses.
Integrating sequence variants and predicted protein structures A theoretical tutorial describing the details of the structure database, how it’s created, and its utility.

Articles, workflows, opinions

Key insights into specific topics and can be useful to more advanced users and 'omics enthusiasts in general.