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SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination

delete2019-03-08
delete22
delete
OA
AI
A
Abbas Jariani
C
Christopher Warth
K
Koen Deforche
P
Pieter Libin
A
Alexei J. Drummond
A
Andrew Rambaut
F
F. A. Matsen
K
Kristof Theys *
DOI：10.1093/ve/vez003delete
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Abstract

Abstract

En 中文
Simulations are widely used to provide expectations and predictive distributions under known conditions against which to compare empirical data. Such simulations are also invaluable for testing and comparing the behaviour and power of inference methods. We describe SANTA-SIM, a software package to simulate the evolution of a population of gene sequences forwards through time. It models the underlying biological processes as discrete components: replication, recombination, point mutations, insertion-deletions, and selection under various fitness models and population size dynamics. The software is designed to be intuitive to work with for a wide range of users and executable in a cross-platform manner.
Keywords:
mutation
selection
fitness
simulation
recombination
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Key information extracted from the uploaded paper, including a brief overview, abstract, background, key highlights, visual analysis, and future outlook.

Journal

Virus Evolution cover
Virus Evolution
IF:
4
Papers:
957
Citations:
3.6K

Organization

F
Fred Hutchinson Cancer Center
Scholars:
1.2W
Papers: 9.3K
Citations: 18
K
KU Leuven
Scholars:
5.7W
Papers: 5.2W
Citations: 8.1W
V
Vrije Universiteit Brussel
Scholars:
1.4W
Papers: 1.3W
Citations: 129
U
University of Edinburgh
Scholars:
5.2W
Papers: 4.6W
Citations: 71
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