FORESTER 1.9

forester.tools
Class DoRIO

java.lang.Object
  |
  +--forester.tools.DoRIO

public class DoRIO
extends java.lang.Object

Version:
1.200 -- last modified: 10/01/01
Author:
Christian M. Zmasek

Constructor Summary
DoRIO()
           
 
Method Summary
static void main(java.lang.String[] args)
          Main method to call RIO.inferOrthologs(Tree,Tree), followed by RIO.inferredOrthologsToString(String,boolean).
 
Methods inherited from class java.lang.Object
, clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

DoRIO

public DoRIO()
Method Detail

main

public static void main(java.lang.String[] args)
Main method to call RIO.inferOrthologs(Tree,Tree), followed by RIO.inferredOrthologsToString(String,boolean).

Clumsy method, btw.

(Last modified: 07/05/01)

args[ 0 ] - args[ 11 ] use the following tags.
M= (String) Multiple gene tree file name (mandatory)
N= (String) Query, seq name of seq whose orthologs are to be inferred (mandatory)
S= (String) Species tree file name
O= (String) Output file name (overwrites without warning!)(mandatory)
D= (String) Distance matrix file for pairwise distances
d= (String) Distance list file for distances to query (instead of "D=")
T= (String) tree file for distances of orthologs to LCA
of orthologs and for mean bootstrap value (if t= is not used),
must be binary
t= (String) Tree file for mean bootstrap value (if this option is used,
the mean bootstrap value is not calculated from the tree read in
with T=), not necessary binary
I           Save the rooted, with dup vs spec and orthology information
decorated consensus tree read in with T=
as output-file-name.rio.nhx
P= (int) Sort priority
L= (double) Threshold orthologs for output (use ' for doubles. e.g.'Y=5.5')
R= (double) Threshold "super orthologs" for output
U= (double) Threshold orthologs for distance calculation
V= (double) Threshold "super orthologs" for distance calculation
X= (int) More than one ortholog:
numbers of sd the dist. to LCA has to differ from mean
to generate a warning
Y= (int) No orthologs:
numbers of sd the dist to root has to differ from mean
to generate a warning
Z= (double) One ortholog:
threshold for factor between the two distances to their
LCA (larger/smaller) to generate a warning

FORESTER 1.9