forester v1.4

forester.tools
Class DoRIO

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

public class DoRIO
extends java.lang.Object

Version:
1.000 -- last modified: 12/11/00
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 v1.4