DESCRIPTION

Package: cognac
Type: Package
Title: Core Gene Alignment Concatenation
Version: 1.0
Date: 2020-05-18
Author: Ryan D. Crawford
Maintainer: Your Name <rcrawfo@umich.edu>
Description: Implimention of a method to create a concatenated gene alignment 
   of phylogenetic marker genes in R with integration of c++ via Rcpp and
   multi-threadding enabled with tbb via RcppParallel, and in R via the 
   future package. Genomic data is input and the coding sequences are 
   extracted and translated. CD-HIT is used to identify orthologous genes,
   and common phylogenetic marker genes are identified. These genes are then 
   aligned with mafft individually and the algnments are then concatenated.
   Optionally the alignment can then be reverse translated to create a 
   nucleotide alignment.
License: GPL (>= 2)
Imports: 
    Rcpp (>= 1.0.3), 
    RcppParallel (>= 4.4.4),
    future (>= 1.15.1),
    future.apply(>= 1.3.0),
    ape(>= 5.3)
LinkingTo: Rcpp, RcppParallel
SystemRequirements: GNU make
Encoding: UTF-8
RoxygenNote: 7.1.1