clustalw2

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Type clustalw2 at the command prompt and you will get the following screen:

**************************************************************
******** CLUSTAL 2.1 Multiple Sequence Alignments  ********
**************************************************************
    1. Sequence Input From Disc
    2. Multiple Alignments
    3. Profile / Structure Alignments
    4. Phylogenetic trees
    S. Execute a system command
    H. HELP
    X. EXIT (leave program)

   Your choice: 1
   Sequences should all be in 1 file.
   7 formats accepted:
   NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF, RSF.
   Enter the name of the sequence file :

   Your choice: 2
   ****** MULTIPLE ALIGNMENT MENU ******
   1.  Do complete multiple alignment now Slow/Accurate
   2.  Produce guide tree file only
   3.  Do alignment using old guide tree file
   4.  Toggle Slow/Fast pairwise alignments = SLOW
   5.  Pairwise alignment parameters
   6.  Multiple alignment parameters
   7.  Reset gaps before alignment? = OFF
   8.  Toggle screen display          = ON
   9.  Output format options
   I. Iteration = NONE
   S.  Execute a system command
   H.  HELP
   or press [RETURN] to go back to main menu

   Your choice: 3
   ****** PROFILE AND STRUCTURE ALIGNMENT MENU ******
   1.  Input 1st. profile
   2.  Input 2nd. profile/sequences
   3.  Align 2nd. profile to 1st. profile
   4.  Align sequences to 1st. profile (Slow/Accurate)
   5.  Toggle Slow/Fast pairwise alignments = SLOW
   6.  Pairwise alignment parameters
   7.  Multiple alignment parameters
   8.  Toggle screen display                = ON
   9.  Output format options
   0.  Secondary structure options
   S.  Execute a system command
   H.  HELP
   or press [RETURN] to go back to main menu

   Your choice: 4
   ****** PHYLOGENETIC TREE MENU ******
   1.  Input an alignment
   2.  Exclude positions with gaps?        = OFF
   3.  Correct for multiple substitutions? = OFF
   4.  Draw tree now
   5.  Bootstrap tree
   6.  Output format options
   7.  Clustering algorithm = NJ
   S.  Execute a system command
   H.  HELP
   or press [RETURN] to go back to main menu