reyes

<p>A dataset containing the sequences of mtDNA-encoded proteins from different mammalian species (Reyes et al. 1996, Mol.Biol. Evol. 17:979)</p>

datasets

Contains utilities for the analysis of protein sequences in a phylogenetic context.
Allows   the generation of phylogenetic trees base on protein sequences in an alignment-independent way.
Two different methods have been implemented. One approach is based on the frequency analysis of n-grams,
previously described in Stuart et al. (2002) <doi:10.1093/bioinformatics/18.1.100>. The other approach is based on the species-specific neighborhood preference around amino acids. Features include the conversion of a protein set into a vector
reflecting these neighborhood preferences, pairwise distances (dissimilarity) between these vectors,
and the generation of trees based on these distance matrices.

Juan Aledo

EnvNJ

Whole Genome Phylogenies Using Sequence Environments

Juan Carlos Aledo

reyes function

<p>A data frame with 13 rows (one per protein) and 34 variables (one per species)</p>

reyes: 13 orthologous mtDNA-encoded proteins of 34 mammalian species.

Description

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