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Update README.md
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shajoezhu committed Aug 26, 2014
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Expand Up @@ -54,8 +54,8 @@ Options | Useage |
-o STR _[option]_ | Specify the file name prefix for simulated gene trees. Prefix is set as "OUT" by **default**, When options are not specified, only output trees with branch lengths are in coalescent unit.|
-_sim\_mut\_unit_ | Convert the simulated gene tree branch lengths to mutation unit.|
-_sim\_num\_gener_ | Convert the simulated gene tree branch lengths to number of generations.|
_-sim\_num\_mut_ | Simulate numbers of mutations on each branch of simulated gene trees.|
_-sim\_Si\_num_ | Generate a table, which includes the number of segregating sites and the total branch length of the gene tree, as well as the TMRCA.|
-_sim\_num\_mut_ | Simulate numbers of mutations on each branch of simulated gene trees.|
-_sim\_Si\_num_ | Generate a table, which includes the number of segregating sites and the total branch length of the gene tree, as well as the TMRCA.|
-f | Generate a topology frequency table of a set of input trees or simulated gene trees. |
-gt STR | Specify the FILE NAME of trees to analyse tree topology frequencies.|
-seg | Generate segregating site data.|
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