The software consists of two parts. A Python script for estimating the
HMMs called tain_rank.py and the trainmet R-package which serves as an
(optional) wrapper for train_rank.py and performs statistic
summarization and visualization.

To use it, first install all dependencies for train_rank.py as
described in
http://www.cin.ufpe.br/~igcf/Metabolites/scripts/hmm/readme.txt. 

Only Linux/MacOSX are supported.

Then, install the trainmet R-package's dependencies Biobase and pls by
starting R and calling

#+begin_src R
  source("http://www.bioconductor.org/biocLite.R")
  biocLite("Biobase")
  install.packages("pls")
#+end_src

then, install trainmet by in a shell calling

#+begin_src sh 
  wget http://www.cin.ufpe.br/~igcf/Metabolites/scripts/trainmet_0.0.3.tar.gz
  R CMD INSTALL trainmet_0.0.3.tar.gz
#+end_src

for a brief demonstration of the package do:

#+begin_src R
  library(trainmet)
  openVignette("trainmet")
#+end_src