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java.lang.Object | +--forester.tools.DoRIO
Constructor Summary | |
DoRIO()
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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 |
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Constructor Detail |
public DoRIO()
Method Detail |
public static void main(java.lang.String[] args)
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
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FORESTER 1.9 | |||||||
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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |