alview

a matrix or a list of DNA sequences (class <code>"DNAbin"</code>).

a character string giving the name of the file where to print the sequences; by default, they are printed in the console.

file

a logical specifying whether to print the bases as uppercase letters.

uppercase

This function displays in the console or a file an alignment of DNA sequences. The first sequence is printed on the first row and the bases of the other sequences are replaced by dots if they are identical with the first sequence.

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 allelic and nucleotide data, 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. 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) whose results are returned into R.

alview: Print DNA Sequence Alignements

Description

Usage

Arguments

Details

See Also

Examples