pathd8: Tree relative datation with PATHd8

In fkeck/diatobc: Bioinformatic toolbox for my projects

Description

This function uses PATHd8 to date phylogenetic trees with the Mean Path Length algorithm.

Usage

pathd8(phy, pathd8.exec)

Arguments

phy	a phylogenetic tree (class phylo) to date.
pathd8.exec	a character string giving the path of the program.

Details

This is a limited wrapper of the C program PATHd8 to perform tree datation in relative time with the Mean Path Length algorithm. Wrapper for calibrated datation (D8) is not implemented.

Value

An ultrametric tree of class phylo.

References

• Britton, T., Anderson, C. L., Jacquet, D., Lundqvist, S., & Bremer, K. (2007). Estimating divergence times in large phylogenetic trees. Systematic biology, 56(5), 741-752.

• Britton, T., Oxelman, B., Vinnersten, A., & Bremer, K. (2002). Phylogenetic dating with confidence intervals using mean path lengths. Molecular phylogenetics and evolution, 24(1), 58-65.

fkeck/diatobc documentation built on May 12, 2019, 7:18 p.m.