thiberio/evolsimindex repository overview

⁠Evolutionary Similarity Index

Assess evolutionary similarity between gene families

⁠Overview

Evolutionary Similarity Index () is a metric for evolutionary similarity between gene families. It is the product of

• : is the coefficient of determination from an weighted Orthogonal Distance Regression

• : is , where is the Bray-Curtis dissimilarity between two gene families.

is less susceptible to phylogenetic noise than its tree-based counterparts, and more computationally efficient given that it bypasses tree reconstruction.

Preprint avaialable on bioRxiv: https://doi.org/10.1101/2020.10.16.343293⁠.

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⁠Getting started

Click the "Open in Colab" button above to get started.

Press ⌘+F9 or CTRL+F9 to run all cells, and fill the required parameters in the botton. Alternatively, press SHIF+ENTER to run each cell at a time. Have fun!

⁠Docker

Available on Docker Hub⁠

docker pull thiberio/evolsimindex to download container...

... once downloaded, run docker run -p 8888:8888 thiberio/evolsimindex and follow terminal instructions. Jupyter notebook will be available at http://127.0.0.1:8888