Add in-review phylotrack link

Author: mmore500

blog_efflux/_posts/2023-08-10-dolson2023phylotrack.md

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+---
+layout: efflux
+title: 'Phylotrack: C++ and Python libraries for "in silico" phylogenetic tracking'
+date: 2023-08-10
+permalink: "/pubs/:title"
+category: preprint
+download: https://github.com/openjournals/joss-papers/blob/joss.05754/joss.05754/10.21105.joss.05754.pdf
+doi: "10.21105/joss.04866"
+authors:
+  - Emily Dolson
+  - Santiago Rodriguez-Papa
+  - Matthew Andres Moreno
+venue: Journal of Open Source Software
+projects:
+  - hstrat
+abstract: |
+  In silico evolution instantiates the processes of heredity, variation, and differential reproductive success (the three "ingredients" for evolution by natural selection) within digital populations of computational agents.
+  Consequently, these populations undergo evolution, and can be used as virtual model systems for studying evolutionary dynamics.
+  This experimental paradigm --- used across biological modeling, artificial life, and evolutionary computation --- complements research done using in vitro and in vivo systems by enabling the user to conduct experiments that would be impossible in the lab or field [@dolsonDigitalEvolutionEcology2021].
+  One key benefit is complete, exact observability.
+  For example, it is possible to perfectly record the full set of parent-child relationships over the history of a population, yielding precise and accurate phylogenies (ancestry trees).
+  This information reveals the sequences of events behind gain, loss, or maintenance of specific traits, and also facilitates making inferences about the underlying evolutionary dynamics of a given system.
+
+  The Phylotrack project provides libraries for tracking and analyzing phylogenies in in silico evolution.
+  The project is composed of 1) Phylotracklib: a header-only C++ library, developed under the umbrella of the Empirical project, and 2) Phylotrackpy: a Python wrapper around Phylotracklib, created with Pybind11.
+  Both components supply a public-facing API to attach phylogenetic tracking to digital evolution systems, as well as a stand-alone interface for measuring a variety of popular phylogenetic topology metrics.
+  The underlying algorithm design prioritizes efficiency, allowing Phylotrack to support large agent populations with rapid generational turnover.
+  The underlying C++ implementation ensures fast, memory-efficient performance, with multiple explicit features (e.g., phylogeny pruning and abstraction, etc.) for reducing the memory footprint of phylogenetic information.
+bibtex: |-
+  in review
+citation: in review
+---