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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