bird.orders


  This data set describes the phylogenetic relationships of the orders
  of birds as reported by Sibley and Ahlquist (1990). Sibley and
  Ahlquist inferred this phylogeny from an extensive number of DNA/DNA
  hybridization experiments. The ``tapestry'' reported by these two
  authors (more than 1000 species out of the ca. 9000 extant bird
  species) generated a lot of debates.<p></p><p>  The present tree is based on the relationships among orders. The
  branch lengths were calculated from the values of $Delta T50H$ as found in Sibley and Ahlquist (1990,
  fig. 353).
</p>

datasets

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle, MAFFT) whose results are returned into R.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

bird.orders function

The data are stored as an object of class <code>"phylo"</code> which
  structure is described in the help page of the function
  <code><a rd-options="" href="/link/read.tree?package=ape&version=4.0" data-mini-rdoc="ape::read.tree">read.tree</a></code>.

Format

Sibley, C. G. and Ahlquist, J. E. (1990) Phylogeny and classification
  of birds: a study in molecular evolution. New Haven: Yale University Press.

Source


  This data set describes the phylogenetic relationships of the orders
  of birds as reported by Sibley and Ahlquist (1990). Sibley and
  Ahlquist inferred this phylogeny from an extensive number of DNA/DNA
  hybridization experiments. The ``tapestry'' reported by these two
  authors (more than 1000 species out of the ca. 9000 extant bird
  species) generated a lot of debates.

  The present tree is based on the relationships among orders. The
  branch lengths were calculated from the values of $Delta T50H$ as found in Sibley and Ahlquist (1990,
  fig. 353).


The data are stored as an object of class <code>"phylo"</code> which
  structure is described in the help page of the function
  <code><a rd-options='' href='read.tree'>read.tree</a></code>.

bird.orders: Phylogeny of the Orders of Birds From Sibley and Ahlquist

Description

Usage

Arguments

Format

Source

See Also

Examples