BOXSHADE

BOXSHADE is a program for pretty-printing multiple alignment output. The program itself doesn't do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for BOXSHADE. Of course, you can also use manually aligned sequences (in a proper format. INPUT = aligned sequence files

Manual: http://www.ch.embnet.org/software/BOX_doc.html

Test Input File

126742336      -------ATGGTGCTGTCTCCCGCTGACAAGGCCAACGTCAAGGCCGCCTGGGGCAAGGT 
110005943      ACCCACCATGGTGCTGTCTGCCGCCGACAAGTCCAATGTCAAGGCCGCCTGGGGCAAGGT 
66865969       -------ATGGTGCTGTCTGCCGCCGACAAGTCCAATGTCAAGGCCGCCTGGGGCAAGGT 
                      ************ **** ****** **** *********************** 

126742336      CGGGGGCCACGCCGGCGAGTATGGCGCCGAGGCCCTGGAGAGG-----------------
110005943      TGGCGGCAACGCTGGAGCTTATGGCGCAGAGGCTCTGGAGAGG-----------------
66865969       TGGCGGCAACGCTCCAGCTTTTGGCGCAGAGGCCCTGGAGAGGTGAGCACCGCACCTGCC
                ** *** ****    *  * ****** ***** *********                 

126742336      ------------------------------------------------------------
110005943      ------------------------------------------------------------
66865969       CCGCGGGGATCGGGCCGCACGCCGGGCGCGTCCTTGTCCCGGGCCGCCCGGCCTAAGCCC

 

126742336      ------------------------ATGTTCCTGAGCTTCCCCACCACCAAGACCTACTTC 
110005943      ------------------------ATGTTCCTGAGCTTCCCCACCACCAAGACCTACTTC 
66865969       AGTTCTCCTGCCTCTTCACCCAGGATGTTCCTGAGCTTCCCCACCACCAAGACCTACTTC 
                                       ************************************ 

126742336      CCCCACTTCGACGTGACCCACGGCTCCGCCCAGGTCAAGGCCCACGGCAAGAAGGTGGCC 
110005943      CCCCACTTCGACCTGAGCCACGGCTCCGCCCAGGTCAAGGGCCACGGCGAGAAGGTGGCC 
66865969       CCCCACTTCGACCTGAGCCACGGCTCCGCCCAGGTCAAGGCCCACGGCGAGAAGGTGGCC 
               ************ *** *********************** ******* *********** 

126742336      GATGCCCTCACCCAGGTCGTCGACCACTTGGACGACCTGCCCGGCGCCCTGTCCGCGCTC
110005943      GCCGCGCTGACCAAAGCGGTGGGCCACCTGGACGACCTGCCCGGTACCCTGTCTGATCTG
66865969       AACGCGCTGACCAAAGCGGTGGGCCACCTGGACGATCTGCCCGGTACCCTGTCTGATCTG
                  ** ** *** * *  ** * **** ******* ********  ******* *  ** 

126742336      AGCGACCTGCACGCCCAAAAGCTGCGGGTGGACCCTGTTAACTTCAAG------------
110005943      AGTGACCTGCACGCCCACAAGCTGCGTGTGGACCCGGTCAACTTCAAG------------
66865969       AGTGACCTGCACGCTCACAAGCTGCGTGTGGACCCGGTCAACTTCAAGGTGAGCTCGCGG
               ** *********** ** ******** ******** ** *********            

126742336      ------------------------------------------------------------
110005943      ------------------------------------------------------------
66865969       GCTGGGCCGGGACAGATCTGGGCTAGAGGGGCAGAGAATGCGGAGGCGCCCCCACCCAGC

 

126742336      --------------------------------CTCCTGGCTCACTGCCTGCTGGTGACCC 
110005943      --------------------------------CTTCTGAGCCACACCCTGCTGGTGACCC 
66865969       CCCAGCCCCCCTGACGTCTCCTCTCTCGGCAGCTTCTGAGCCACACCCTGCTGGTGACCC 
                                               ** ***   ***  ************** 

126742336      TGGCCAACCACCACCCCAATGAATTCACTCCTGCGGTGCACGCCTCCCTGGACAAGTTCC
110005943      TGGCCTGCCACCTCCCCAATGATTTCACCCCCGCCGTCCACGCCTCCCTGGACAAGTTCT
66865969       TGGCCTCCCACCTCCCCAATGATTTCACCCCCGCGGTCCACGCCTCCCTGGACAAGTTCT
               *****  ***** ********* ***** ** ** ** ********************* 

126742336      TGGCCAACGTGAGCACCGTGCTCACCTCCAAGTATCGTTAA-------------------
110005943      TGGCCAGCGTGGGCACCGTGCTGACCTCCAAATACCGTTAAGCTGGGGCCTCGACGACCC
66865969       TGGCCAACGTGAGCACCGTGCTGACCTCCAAATACCGTTAA-------------------
               ****** **** ********** ******** ** ******                   

126742336      -----------------------------------------------
110005943      CCTACCCTGGCCTGGAGCGCCCTTGCGCTCTGCGCACTCTCACCTCC
66865969       -----------------------------------------------

Test Output File