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