http://evolution.gs.washington.edu/phylip/getme.html

= 【說明】 =



= 【安裝】 =
預先安裝套件：
 * libx11-dev、libxaw

{{{
    wget http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz
    tar zxvf phylip-3.69.tar.gz
    cd src
    make install
}}}

= 【測試一】 =
 1. 指令：
   {{{
cp HCV.phy infile
seqboot
   }}}
   畫面：
   {{{
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
   }}}
 1. 指令：
   {{{
y 
   }}}
   畫面：
   {{{
Random number seed (must be odd)?   
   }}}
 1. 指令：
   {{{
5
   }}}
   畫面：
   {{{
completed replicate number   10
completed replicate number   20
completed replicate number   30
completed replicate number   40
completed replicate number   50
completed replicate number   60
completed replicate number   70
completed replicate number   80
completed replicate number   90
completed replicate number  100

Output written to file "outfile"

Done.
   }}}
   輸出：outfile

= 【測試二】 =
 1. 指令：
    {{{
mv outfile infile
dnapars
    }}}
    畫面：
    {{{
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
    }}}
 1. 指令：
    {{{
Y
    }}}
    輸出 "outfile" 、 "outtree"：

= 【測試三】 =
 1. 指令：
    {{{
mv outtree intree
consense
    }}}
    畫面：
    {{{
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) 
    }}}
 1. 指令：
    {{{
A
    }}}
    畫面：
    {{{
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)
    }}}
 1. 指令：
    {{{
Y
    }}}
    畫面：
    {{{
Consensus tree written to file "outtree"

Output written to file "outfile"

Done.
    }}}
    輸出： "outtree" 、 "outfile"