ligotree: Maximum likelihood tree for 13 _Ligophorus_ species

In monogeneaGM: Geometric Morphometric Analysis of Monogenean Anchors

Description

This data set contains the maximum likelihood (Felsenstein, 1981) phylogenetic tree of 13 Ligophorus species, inferred using concatenated 18S rRNA, ITS1 rRNA and 28S rRNA DNA sequences (10 000 bootstrap replicates). The best DNA substitution model was GTR+G. Multiple sequence alignment was done using online MAFFT server (Version 7; Katoh, 2013; Katoh & Standley, 2013) with default parameters. Maximum likelihood tree construction was done using IQ-TREE (Minh et al., 201; Nguyen et al., 2015).

Usage

data(ligotree)

Format

A phylo object, so the ape package (Paradis et al., 2004) needs to be installed

Details

The phylogenetic tree comes with bootstrap support for the internal nodes.

Author(s)

Tsung Fei Khang [e-mail]

Source

Khang TF, Soo OYM, Tan WB, Lim LHS. (2016). Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution. PeerJ 4:e1668.

Khang TF, Soo OYM, Tan WB, Lim LHS. (2016). Data from: Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.50sg7.

References

Felsenstein J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution 17: 368-376.

Katoh K. (2013). MAFFT - a multiple sequence alignment program. Available at http://mafft.cbrc.jp/alignment/server.

Katoh K, Standley DM. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution 30: 772-780.

Minh BQ, Nguyen MAT, Von Haeseler A. (2013). Ultrafast approximation for phylogenetic bootstrap. Molecular Biology and Evolution 30: 1188-1195.

Nguyen L-T, Schmidt HA, Von Haeseler A, Minh BQ. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Molecular Biology and Evolution 32: 268-274.

Paradis E, Claude J & Strimmer K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.

See Also

tpColorPlot2d

Examples

library(ape)

data(ligotree)
plot.phylo(ligotree, show.node.label=TRUE)

Example output

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 

monogeneaGM documentation built on May 29, 2017, 9:18 p.m.