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

#at first, copy HCV.phy and name the new copy "infile"

cp HCV.phy infile

#exert the following command line:

seqboot

#You will see the following messages, just type "Y" to accept those paramaters
#
########################################################
#Bootstrapping algorithm, version 3.69
#
#Settings for this run:
#  D      Sequence, Morph, Rest., Gene Freqs?  Molecular sequences
#  J  Bootstrap, Jackknife, Permute, Rewrite?  Bootstrap
#  %    Regular or altered sampling fraction?  regular
#  B      Block size for block-bootstrapping?  1 (regular bootstrap)
#  R                     How many replicates?  100
#  W              Read weights of characters?  No
#  C                Read categories of sites?  No
#  S     Write out data sets or just weights?  Data sets
#  I             Input sequences interleaved?  Yes
#  0      Terminal type (IBM PC, ANSI, none)?  ANSI
#  1       Print out the data at start of run  No
#  2     Print indications of progress of run  Yes
#
#  Y to accept these or type the letter for one to change
###############################################################

Y

#Then you will see the following messages, just type "5"
#
########################## 
#Random number seed (must be odd)?
##########################

5

#if seqboot do well, it will generate one file named "outfile", rename "outfile" to "infile" (replace the original "infile")

mv outfile infile

#then, exert the following command line

dnapars

#Again, you will see similar messages and just enter "Y" to accept all paramaters
#
##################################################################
#DNA parsimony algorithm, version 3.69
#
#Setting for this run:
#  U                 Search for best tree?  Yes
#  S                        Search option?  More thorough search
#  V              Number of trees to save?  10000
#  J   Randomize input order of sequences?  No. Use input order
#  O                        Outgroup root?  No, use as outgroup species  1
#  T              Use Threshold parsimony?  No, use ordinary parsimony
#  N           Use Transversion parsimony?  No, count all steps
#  W                       Sites weighted?  No
#  M           Analyze multiple data sets?  No
#  I          Input sequences interleaved?  Yes
#  0   Terminal type (IBM PC, ANSI, none)?  ANSI
#  1    Print out the data at start of run  No
#  2  Print indications of progress of run  Yes
#  3                        Print out tree  Yes
#  4          Print out steps in each site  No
#  5  Print sequences at all nodes of tree  No
#  6       Write out trees onto tree file?  Yes
#
#  Y to accept these or type the letter for one to change
##################################################################

Y

#if dnapars work well, it will generate two files named "outfile" and "outtree", rename "outtree" to "intree"

mv outtree intree

#then, exert the following command line

consense

#you will see the following message, just type "R"
#
#####################################################
#consense: the file "outfile" that you wanted to
#     use as output file already exists.
#     Do you want to Replace it, Append to it,
#     write to a new File, or Quit?
#     (please type R, A, F, or Q)
###################################################

A

#and then you will see the following messages, type "Y" to accept all paramaters
#
########################################################################
#Consensus tree program, version 3.69
#
#Settings for this run:
# C         Consensus type (MRe, strict, MR, Ml):  Majority rule (extended)
# O                                Outgroup root:  No, use as outgroup species  1
# R                Trees to be treated as Rooted:  No
# T           Terminal type (IBM PC, ANSI, none):  ANSI
# 1                Print out the sets of species:  Yes
# 2         Print indications of progress of run:  Yes
# 3                               Print out tree:  Yes
# 4               Write out trees onto tree file:  Yes
#
#Are these settings correct? (type Y or the letter for one to change)
###########################################################################

Y

#if consense work well, it will generate two files named "outfile" and "outtree",
#please refer to 2_dnapars_3_consense_outfile and check if the content of "outfile" is indentical to that of 2_dnapars_3_consense_outfile.