Install r-Coffee

Use the r-Coffee shipped with the tutorial (downloads-folder) and use the provided installer to set up your local r-Coffee.

  $ ./install rcoffee

The installation script tells you where you can find the executables and what you should add to your PATH variable.

Afterwards align the four.seq using r_coffee and compare the output with the one given by LocARNA.

  $ t_coffee four.seq > r_coffee.out

 [r_coffee.out]
 CLUSTAL FORMAT for T-COFFEE Version_9.03.r1318 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=74, Nseq=4, Len=74 

 M10740          GCGGAUUUAGCUCAGUU-GGGAGAGCGCCAGACUGAAGAUUUGGAGGUCC
 K00349          GCCGAAAUAGCUCAGUU-GGGAGAGCGUUAGACUGAAGAUCUAAAGGUCC
 K00283          GGGCCGGUAGCUCAUUUAGGCAGAGCGUCUGACUCUUAAUCAGACGGUCG
 AF346993        CAGAGUGUAGCUUAAC---ACAAAGCACCCAACUUACACUUAGGAGAUUU
                        ***** *       * ***     ***     *     * *  

 M10740          UGUGUUCGAUCCACAGAAUUCGCA
 K00349          CCGGUUCAAUCCCGGGUUUCGGCA
 K00283          CGUGUUCGAAUCGCGUCCGGCCCA
 AF346993        CAACUUAACUUGACCG--CUCUGA
                     **                 *\