DESCRIPTION

Package: LDJump
Type: Package
Title: Estimating Variable Recombination Rates from Population Genetic Data
Version: 0.3.1
Imports: adegenet (>= 2.0.1), 
   ape, 
   genetics (>= 1.3.8.1), 
   Biostrings (>= 2.38.4),
	 stepR (>= 2.0.1), 
   vcfR (>= 1.5.0), 
   snow,
   data.table,
   pegas, 
   mgcv
Depends: R (>= 2.10),
	 seqinr (>= 3.1-3),
	 quantreg
Author: Philipp Hermann, Andreas Futschik, Fardokhtsadat Mohammadi
Maintainer: Philipp Hermann <philipp.hermann@jku.at>
Description: This package estimates variable recombination rates from population genetic data. It is a unix based program (with a necessary installation of LDhat), able to estimate the recombination map of sequences in fasta and vcf format. Sequences are divided in short segments of user defined length. The recombination rate is estimated for every segment with a regression model. This set of estimates is fed in a segmentation algorithm (SMUCE) to estimate the breakpoints of the recombination landscape. Moreover, populations can be simulated under user input demographic scenarios in order to train the regression model of constant recombination rates. 
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 6.1.1
BugReports: https://github.com/PhHermann/LDJump/
SystemRequirements: Unix Operating System, PhiPack, LDhat (Version 2.2, optional), dos2unix, awk, [For simulations: scrm, ms2dna (Version 1.16)]