FORESTER 1.6

forester.tools
Class DoRIO

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

public class DoRIO
extends java.lang.Object

Version:
1.001 -- last modified: 01/11/01
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). (Last modified: 12/04/00) args[ 0 ] - args[ 11 ] use the following tags. M= (String) multiple gene tree file name (mandatory*)** N= (String) seq name of seq whose orthologs are to be inferred (mandatory) S= (String) species tree file name (mandatory) O= (String) output file name (overwrites without warning!)(mandatory) D= (String) distance matrix file for pairwise distances** T= (String) (consensus) tree file for distances of orthologs to LCA of orthologs** I save the rooted, with dup vs spec and orthology information decorated tree read in with T= as output-file-name.nhx P= (int) sort priority Q= (double) threshhold orthologs, (use ' for doubles. e.g. 'Y=5.5') R= (double) threshhold "super orthologs" 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 A= (String) "all" path/name without suffix for ** (mlt,dst,nhx) unless path/name is given with A= Example. DoRIO A=pfam_trees/trees112900full100x_100/E1_dehydrog N=ODPA_KLULA/78-370 P=5 Q=0 R=90 O=E1_dehydrog

FORESTER 1.6