Package 'rphast' Title R Interface to Phast Software for Comparative Genomics

December 13, 2013 Copyright The code in src/pcre is Copyright (c) 1997-2010 University of Cambridge. All other code is Copyright (c) 2002-2010 University of California, Cornell University. Maintainer Melissa Hubisz License BSD_3_clause + file LICENSE Title R interface to PHAST software for comparative genomics Author Melissa Hubisz, Katherine Pollard, and Adam Siepel Description RPHAST is an R interface to the PHAST package (Phylogenetic Analysis with Space/Time Models). It can be used for many types of analysis in comparative and evolutionary genomics,such as estimating models of evolution from sequence data, scoring alignments for conservation or acceleration, and predicting elements based on conservation or custom phylogenetic hidden Markov models. It can also perform many basic operations on multiple sequence alignments and phylogenetic trees. Version 1.5 URL http://compgen.bscb.cornell.edu/rphast Date 2011-02-08 Depends stats Suggests ape, seqLogo Collate 'bgc.R' 'checkArgs.R' 'feat.R' 'hmm.R' 'listOfLists.R' 'msa.R' 'optim.R' 'phastCons.R' 'phyloFit.R' 'phyloP.R' 'plot.R' 'rphast.R' 'treeModel.R' 'trees.R' 'zzz.R'