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Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

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Published on: October 16, 2018

ipcoal: an interactive Python package for simulating and analyzing genealogies and sequences on a species tree or

Patrick F McKenzie¹, Deren A R Eaton¹

¹Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA.

Bioinformatics (Oxford, England)

|May 14, 2020

Summary

ipcoal is a free Python package that simulates genealogies and sequences using complex demographic models. It aids in phylogenetic inference, data analysis, and teaching coalescent methods.

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Area of Science:

Computational Biology
Population Genetics
Bioinformatics

Background:

Simulating complex demographic histories is crucial for understanding evolutionary processes.
Existing tools often require extensive scripting to interface with coalescent simulators.
There is a need for user-friendly software to automate the description of demographic models.

Purpose of the Study:

To introduce ipcoal, a Python package for simulating and analyzing genealogies and sequences.
To automate the process of translating species trees/networks into demographic models for coalescent simulation.
To provide tools for downstream analysis, phylogenetic inference, and visualization of simulation results.

Main Methods:

ipcoal parses user-supplied species trees or networks to define demographic models.
It interfaces with the msprime coalescent simulator.
Outputs include genealogies, sequences, and metadata in tabular formats.
Includes automated gene tree inference and visualization tools.

Main Results:

ipcoal facilitates the description of complex demographic models, including divergence times, population sizes, and migration.
Simulated data is readily available for downstream analyses.
Phylogenetic inference and model verification are streamlined.
The package supports posterior predictive data analysis and methods validation.

Conclusions:

ipcoal is a versatile and open-source tool for simulating and analyzing population genetic data.
It simplifies the application of coalescent theory in research and education.
The package enhances the ability to test evolutionary hypotheses and validate computational methods.