About

orthofisher extracts and determines the copy number of a predetermined set of orthologs, which can be used for the identification of single copy orthologous genes or estimation of gene family copy number.


Performance Assessment

Using 1,530 sequence similarity searches across six model eukaryotic proteomes, the performance of orthofisher was compared to results obtained from BUSCO. Examination of precision and recall revealed near perfect performance. More specifically, orthofisher had a recall of 1.0 and precision of 0.99. Precision is less than 1.0 because priors of expected sequence length and sequence similarity scores–which are not implemented in orthofisher–resulted in more missing genes in the BUSCO pipeline than the orthofisher pipeline.

We also compared the orthofisher and BUSCO pipelines to OrthoFinder and found all three performed similarly. Details about similarities and differences can be examined further in our manuscript.


The Team

orthofisher is developed and maintained by Jacob L. Steenwyk with guidance and invaluable suggestions from Antonis Rokas.


JLSteenwyk

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Jacob L. Steenwyk is a Howard Hughes Medical Institute Gilliam fellow in the Antonis Rokas Laboratory at Vanderbilt University. His research foci include understanding the parameters that influence genome stability, the genomics of microbial domestication, and the evolution of pathogenicity. Beyond research, Steenwyk aims to make education more accessible through diverse avenues of community engagement. Find out more information at his personal website.


ARokas

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Antonis Rokas is the Cornelius Vanderbilt Chair in Biological Sciences and Director of the Evolutionary Studies Initiative at Vanderbilt University. Research in his laboratory focuses on the study of the DNA record to gain insight into the patterns and processes of evolution. Using a combination of computational and experimental approaches, his lab’s current research aims to understand the molecular foundations of the fungal lifestyle, the reconstruction of the tree of life, and the evolution of human pregnancy. Find out more information at his laboratory’s website.