phylip.txt

比对算法的具体应用DNA序列分析 ——基因序列 ——基因表达调控信息 寻找基因牵涉到两个方面的工作 ： 识别与基因相关的特殊序列信号 预测基因的编码区域 结合两个方面的结果确定基因的位置和结构 基因表

***  GENOME EXPLORER HELP FILE  ***

To provide help on using the GUI, and information about how the programs run

Contents

1)  Outline of Function
2)  Parameters loaded from the .inf file (settings menu)
3)  The User Interface
4)  Underlying Method


---  PHYLIP  ---

---  1)  Outline of Function ---

Consecutively run any of the programs within phylip where the outfile from one
program serves as the infile for the next.

Many infiles can be selected for the first file in the chain, then each file in
turn will pass through all the desired programs before the next begins.

Phylip documentation is extensive and thorough.  Buttons are provided on the gui
to open phylip documentation for the program currently selected in that tab pane.

---  2)  Parameters loaded from the .inf file (settings menu) ---


phyDocDir          path to the directory in which all phylip documentation files are located

phyInDir           path to the directory in which to open the infile file chooser

phyOutDir          path to the default directory in which to write all outfiles

phylipExeDir       path to the directory in which all phylip executables are located

phylipTempDir      path to the directory in which to create a new directory (based on
                   date and time) to which all temp files will be written.  Because
                   phylip is an annoying program. without a command line interface,
                   lots of temp files need to be written.


---  3)  The User Interface  ---


Program Selector tab


type of input file
     select from:
       1)  aligned sequences:  in phylip (.phy) format
       2)  distance matrix files:  produced using dnadist, protdist or chromtree
       3)  new Hampshire format tree files:  produced by neighbor, fitch, kitsch 
           or others
 		 this selection effects the	options available in the check list below

check boxes
     tick the boxes for the type of programs you would like on consecutively on your 
     data.  Select actual programs and parameters in the enabled tab panes


Input Files tab


select input files
     add / remove files from the list box using the add / remove buttons.   
     Ensure you select the infiles in the CORRECT FORMAT for the FIRST type of
     program you are running

directory for seqboot outfiles
     directory to which all seqboot outfiles will be written

directory for distance program outfiles
     directory to which all distance program outfiles will be written

directory for phylogeny program outfiles
     directory to which all phylogeny program outfiles will be written

directory for consense outfiles
     directory to which all consense outfiles will be written

directory for draw tree program outfiles
     directory to which all draw tree program outfiles will be written
     


Seqboot tab

see phylip documentation for explanations of the individual parameters


Distance Matrix Program tab

see phylip documentation for explanations of the individual parameters


Phylogeny Building Program tab

see phylip documentation for explanations of the individual parameters


Consense tab

see phylip documentation for explanations of the individual parameters


Tree Drawing Program tab

see phylip documentation for explanations of the individual parameters


---  4)  Underlying Method   ---


Phylip programs are run from a batch file (*.bat), because they have no command line.
This is a rubbish system and entirely platform specific, but there you go.

A file of key-presses is written for each program being run.  This is then
piped to the program at run time.  It means the options in the drop down lists 
have to be in exactly the right order, or the corresponding number of key-presses
will be wrong, and a different parameter will be selected.

There is no way to force phylip programs to take a specific infile and write a
specific outfile.  All files to be run are therefore copied in turn to the phylip
temp directory and renamed 'infile'  the 'outfile' produced is then copied to the 
name and directory specified by the user, and renamed 'infile' for the next program.