evo_rates: Table of evolutionary rates.

In jackalope: A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator

Table of evolutionary rates.

Description

From Table 1 in Sung et al. (2016).

Usage

evo_rates

Format

A data frame with 15 rows and 8 variables:

domain

Either Bacteria or Eukarya for what type of organism the species is.

species

Species name.

Ge

Effective genome size using only coding DNA.

Gc_Gnc

Effective genome size using coding DNA and non-coding DNA that is under purifying selection.

indels

Rate of insertions and deletions (10^{-10} events per site per generation).

subs

Base-substitution mutation rate (10^{-10} events per site per generation).

Ne

Effective population size (\times 10^{6}).

theta_s

Population mutation rate estimated using \theta_s.

pi_s

Population mutation rate estimated using \pi_s.

Source

\Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/g3.116.030890")}

References

Sung, W., M. S. Ackerman, M. M. Dillon, T. G. Platt, C. Fuqua, V. S. Cooper, and M. Lynch. 2016. Evolution of the insertion-deletion mutation rate across the tree of life. G3: Genes | Genomes | Genetics 6:2583–2591.

jackalope documentation built on Oct. 15, 2023, 9:06 a.m.