#change directory to this folder and exert the following command line:

clustalw2

#Then you'll see the following option, choose "1"
###################################################################
# **************************************************************
# ******** CLUSTAL 2.0.11 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

#after choosing "1", it will ask for input file, type "kinase.fta"
########################################################################
#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 :
#########################################################################

kinase.tfa

#After entering input file, the following messages and options appear, choose "2"
#########################################################################
#Sequence format is Pearson
#Sequences assumed to be PROTEIN
#
#
#Sequence 1: KAPA_MOUSE   350 aa
#Sequence 2: KDCA_DROME   354 aa
#Sequence 3: ARK1_HUMAN   689 aa
#Sequence 4: KGP2_DROME  1088 aa
#Sequence 5: YPK2_YEAST   677 aa
#Sequence 6: VIP_MELGA    444 aa
#Sequence 7: K6A3_HUMAN   740 aa
#Sequence 8: DMK_HUMAN    639 aa
#Sequence 9: KPBG_RABIT   386 aa
#Sequence 10: KCC1_YEAST   446 aa
#Sequence 11: PIM1_HUMAN   313 aa
#Sequence 12: KRAF_DROME   781 aa
#Sequence 13: TRKB_HUMAN   822 aa
#Sequence 14: INSR_HUMAN  1382 aa
#Sequence 15: KPRO_MAIZE   817 aa
#Sequence 16: DAF1_CAEEL   669 aa
#
#
#
# **************************************************************
# ******** CLUSTAL 2.0.11 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:
#######################################################################

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:
################################################################################

1

#
################################################################
#Enter a name for the CLUSTAL output file  [kinase.aln]:
##############################################################

(just press [RETURN])

###############################################################
#Start of Pairwise alignments
#Aligning...
#
#Sequences (1:2) Aligned. Score:  45
#Sequences (1:3) Aligned. Score:  26
#Sequences (1:4) Aligned. Score:  36
#Sequences (1:5) Aligned. Score:  39
#Sequences (1:6) Aligned. Score:  39
#Sequences (1:7) Aligned. Score:  32
#Sequences (1:8) Aligned. Score:  31
#Sequences (1:9) Aligned. Score:  23
#Sequences (1:10) Aligned. Score:  24
.
.
.
.
.
#Sequences (11:14) Aligned. Score:  17
#Sequences (11:15) Aligned. Score:  20
#Sequences (11:16) Aligned. Score:  14
#Sequences (12:13) Aligned. Score:  12
#Sequences (12:14) Aligned. Score:  12
#Sequences (12:15) Aligned. Score:  7
#Sequences (12:16) Aligned. Score:  11
#Sequences (13:14) Aligned. Score:  21
#Sequences (13:15) Aligned. Score:  11
#Sequences (13:16) Aligned. Score:  13
#Sequences (14:15) Aligned. Score:  11
#Sequences (14:16) Aligned. Score:  11
#Sequences (15:16) Aligned. Score:  11
#Enter name for new GUIDE TREE           file   [kinase.dnd]:
##############################################################################

(just press [RETURN])

##############################################################################
#Guide tree file created:   [kinase.dnd]
#
#There are 15 groups
#Start of Multiple Alignment
#
#Aligning...
#Group 1:                     Delayed
#Group 2: Sequences:   2      Score:5585
#Group 3: Sequences:   2      Score:6757
#Group 4: Sequences:   4      Score:4840
#Group 5: Sequences:   5      Score:4243
#Group 6:                     Delayed
#Group 7:                     Delayed
#Group 8:                     Delayed
#Group 9:                     Delayed
#Group 10:                     Delayed
#Group 11:                     Delayed
#Group 12:                     Delayed
#Group 13:                     Delayed
#Group 14:                     Delayed
#Group 15:                     Delayed
#Alignment Score -1627
#
#
#
#Consensus length = 1608
#
#CLUSTAL-Alignment file created  [kinase.aln]
#
#
#CLUSTAL 2.0.11 multiple sequence alignment
#
#
#KAPA_MOUSE      ------------------------------------------------------------
#KDCA_DROME      ------------------------------------------------------------
#YPK2_YEAST      ------------------------------------------------------------
#VIP_MELGA       ------------------------------------------------------------
#K6A3_HUMAN      ------------------------------------------------------------
#PIM1_HUMAN      ------------------------------------------------------------
#KGP2_DROME      MRFCFDRLCFATKRPAQNSNSNAPHSSTTVDAPPRPADVDVATVPVATTAPPPQQPVSNL
#DMK_HUMAN       ------------------------------------------------------------
#KPBG_RABIT      ------------------------------------------------------------
#KCC1_YEAST      ------------------------------------------------------------
#ARK1_HUMAN      ------------------------------------------------------------
#INSR_HUMAN      ------------------------MGTGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCP
#TRKB_HUMAN      ------------------------------------------------------------
#KPRO_MAIZE      ------------------------------------------------------------
#KRAF_DROME      ------------------------------------------------------------
#DAF1_CAEEL      ------------------------------------------------------------
#
#
#
#Press [RETURN] to continue or  X  to stop:
######################################################################

X

#######################################################################
#
#****** 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:
########################################################################

(just press [RETURN])

#########################################################################
#
# **************************************************************
# ******** CLUSTAL 2.0.11 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:
##########################################################################

X

#if clustalw do well, it will generate two files named kinase.aln and kinase.dnd,
#please compare these two files with result_kinase.aln and result_kinase.dnd respectively.
#they should be identical.





