Commit b3f58d93 authored by Elias Dohmen's avatar Elias Dohmen 🎓

UserManual+examples

parent 4b93a7fb
File added
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((Xenopus_tropicalis,(Gallus_gallus,(Loxodonta_africana,(Pan_troglodytes,Bos_taurus)))),Saccharomyces_cerevisiae);
((Xenopus_tropicalis,(Gallus_gallus,(Loxodonta_africana,(Pan_troglodytes,Bos_taurus)))),outgroup);
Exact solutions: 2070
Non-ambiguous solutions: 219
Ambiguous solutions: 188
Complex solutions: 1853
Fusions: 801
Fissions: 385
Terminal Loss: 441
Terminal Emergences: 82
Single Domain Losses: 358
Single Domain Emergences: 222
Exact and non-ambiguous solutions: 2289
Fusion rate: 34.99%
Fission rate: 16.82%
Terminal Loss rate: 19.27%
Terminal Emergence rate: 3.58%
Single Domain Loss rate: 15.64%
Single Domain Emergence rate: 9.70%
Exact solutions: 1960
Non-ambiguous solutions: 211
Ambiguous solutions: 178
Complex solutions: 1770
Fusions: 775
Fissions: 364
Terminal Loss: 406
Terminal Emergences: 69
Single Domain Losses: 432
Single Domain Emergences: 125
Exact and non-ambiguous solutions: 2171
Fusion rate: 35.70%
Fission rate: 16.77%
Terminal Loss rate: 18.70%
Terminal Emergence rate: 3.18%
Single Domain Loss rate: 19.90%
Single Domain Emergence rate: 5.76%
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......@@ -124,10 +124,10 @@ def main( ) :
"2 = fissions\n"
"3 = termLosses\n"
"4 = termEmergences\n"
"5 = singleDomainLosses"
"5 = singleDomainLosses\n"
"6 = singleDomainEmergences")
parser.add_argument("-p", action="store", dest="treeshape", default="r", choices=["c", "r"],
help="shape of the tree, circle or tree format")
help="shape of the tree, circle (c) or tree format (r)")
parser.add_argument("-o", action="store", dest="outputname")
parser.add_argument("-y", action="store", type=str, dest="NodeIDtreeName", default=None, help="Name for output file that shows a tree with all node IDs.")
parser.add_argument("-l", dest="short_legend", help="Writes the legend in two levels for short trees", action="store_true")
......
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