comparetrees.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


---  COMPARE TREES  ---

---  1)  Outline of Function ---


To compare new Hampshire tree files to eachother (for an exact match), and to
an array of subtrees for either exact or clade matches.

Many independent comparisons can be made, and then summarised into a single 
output file.


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


tree file input directory         directory in which to open treefile file chooser

tree file directories directory   directory in which to open directory file chooser

compare trees output directory    path to default output directory


---  3)  The User Interface  ---

select trees to be compared to each other
     Choose this option if you want to select several treefiles to be compared to 
     each other
     
select one treefile of each set to compare
     Choose this option if you want to select one tree file from each set to be
     compared, and then select directories containing similarly named files to be 
     compared.
     
select treefiles to run
     add / remove paths to new Hampshire tree files
     
select directories that contain treefiles with names that start the same way
as the names above, and end with the given extension
     add directories that contain treefiles that begin with the same characters
     as the files selected in the "select treefiles to run" box.  (Begin with - 
     are the same up to the first dot).  Edit the extension to enable the correct 
     files to be identified.  

select output directory
     select a directory to which output files will be written

check for all subtrees within selected treefile
     Choose this option if you want to identify a specific treefile to be used 
     to generate subtrees

semi-colon separated list of subtrees to search for
     Choose this option to enter a semi-colon separated list of subtrees to 
     search for - in new hampshire format
     
use all clades in first treefile as subtrees
     Choose this option to use first tree in each set to be compared as a source
     of subtrees

subtree
     path to treefile, or semi-colon separated list of subtrees - depending on 
     radio button selected

look for exact subtrees
     true to include subtree structure when comparing subtrees, false to ignore 
     structure.  e.g. ((A,B),C) vs ((A,C),B) - no match if including structure, 
     but a match if ignoring structure: boils down to (A,B,C) vs (A,C,B).
     
     
---  4)  Underlying Method   ---


trees are stripped of all branch lengths, bootstrap values and leading underscore
characters in species names.  The contents of every set of parentheses is then 
arranged in alphabetical order.  The trees are then compared directly with 
String.equals method.  If NOT looking for exact subtrees, all parentheses within 
each set of parentheses are removed and the species are arranged alphabetically.
e.g.  ((A,B),C)) and ((C,B),A) both become (A,B,C).  String.equals method is then used
to compare the subtrees.