iferres/phylen: Search Core Genes Using HMMs, Compute Multiple Alignment, Concatenate And Compute Phylogeny

This is a package designed for easly compute a phylogeny with the concatenated alignemnt of a set of pre-computed Hidden Markov Models hits. It uses HMMER 3.1b2 as search engine, MAFFT as aligner, and PHANGORN package as phylogeny inference software. It also provides a couple of functions to download specific sets of curated HMMs from the EggNOG database in order to allow the identification of "core" genes and build the alignment and phylogeny with them.

Getting started

Package details

Maintainer<[email protected]>
LicenseMIT + file LICENSE
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
iferres/phylen documentation built on May 6, 2018, 9:24 a.m.