consensus

either (i) a single object of class <code>"phylo"</code>, (ii) a
    series of such objects separated by commas, or (iii) a list
    containing such objects.

a numeric value between 0.5 and 1 giving the proportion for a
    clade to be represented in the consensus tree.

a logical specifying whether to check the labels
    of each tree. If <code>FALSE</code> (the default), it is assumed that all
    trees have the same tip labels, and that they are in the same order
    (see details).

check.labels


  Given a series of trees, this function returns the consensus tree. By
  default, the strict-consensus tree is computed. To get the
  majority-rule consensus tree, use <code>p = 0.5</code>. Any value between
  0.5 and 1 can be used.


manip

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.

consensus: Concensus Trees

Description

Usage

Arguments

Value

Details

References

See Also