comparetrees2.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 each other.  Provides two output figures
per tree comparison.  One is based on distance, the other on structure. 

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

An output displaying number of occurrences of each group across all comparisons
made, is provided.


---  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.  A tree file can have many trees in it.  They will all be compared
     to the first tree in the first treefile if a different comparison tree is not
     selected (see below).  A single output file is created - detailing the numbers 
     of times each group occurred throughout the comparison.
     
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.  The results of all of these comparisons will be listed in a single
     summary file.
     
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

compare all trees to the treefile selected below
     Choose this option if you want to identify a specific treefile to be used 
     as the standard to which all others are compared.
     
compare all trees to the first tree in the first treefile
     Choose this option to use first tree in each set to be compared as a source
     of subtrees.

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

tolerance on distance comparison
     a distance comparison will be performed using the total branch lengths between
     each pair of species.  To count a match, the values for the two trees being 
     compared must be within this percentage of each other for all species.  (This
     is an entirely pointless comparison and probably won't be here much longer...)

normalise distances
     tick to convert the total branch lengths in any one tree to 100.  This is 
     necessary to get meaningful distance comparison results.

trees are rooted
     tick this if the trees are rooted.
     
write summary only
     tick this to suppress the groups output for each comparison and only write a 
     summary file of distance and structure values.  This is a sensible choice if
     you are comparing lots of different pairs of trees.  If you are comparing lots
     of trees to a single standard comparison tree you probably want to know which 
     groups were present in high numbers - in that case do not select this option.

include stats in summary
     tick this option if you want the numbers the tree comparison algorithm used to
     generate the distance and structure values.  There will be two matrices of values
     for each comparison.
     
---  4)  Underlying Method   ---

To compare new Hampshire tree files to each other.  Provides two output figures
per tree comparison.  One is based on distance, the other on structure. In the 
structure comparison every branch with a length >0 is given a length of 1. 
Both methods compare every branch to see if it exists in both trees. If the
branch does not exist it is given a branch length of 0.

The length of the branch in one tree is then subtracted from the length of the
same branch in the other tree, and the difference squared.  All difference
squared values are added together and the square root taken to give the final 
value.

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