FORESTER 1.92

forester.tools
Class DoRIO

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

public class DoRIO
extends java.lang.Object

Version:
1.220 -- last modified: 02/18/02
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: 02/17/02)

args[ 0 ] - args[ .. ] 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 query 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
p           Output ultra paralogs
v=          Threshold ultra paralogs for output (use ' for doubles. e.g.'v=60'),
default is 50
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.'L=5.5'),
default is 0
B= (double) Threshold subtree neighborings for output, default is 0
U= (double) Threshold orthologs for distance calculation, default is 0
X= (int)    More than one ortholog:
numbers of sd the dist. to LCA has to differ from mean
to generate a warning, default is 2
Y= (int)    No orthologs:
numbers of sd the dist to root has to differ from mean
to generate a warning, default is 2
Z= (double) One ortholog:
threshold for factor between the two distances to their
LCA (larger/smaller) to generate a warning, default is 2

FORESTER 1.92