Updated AliSim (markdown)

Author: heikotree

doc/AliSim.md

@@ -645,7 +645,7 @@ All the options available in AliSim are shown below:
 | `--indel <INS>,<DEL>`  | Set the insertion and deletion rate of the indel model, relative to the substitution rate. |
 | `--indel-size <INS_DIS>,<DEL_DIS>`  | Set the [insertion and deletion size distributions](#insertion-and-deletion-models). By default, AliSim uses `POW{1.7/100}` for a power-law (Zipfian) distribution with parameter `a` of 1.7 and maximum indel size of 100.|
 | `--no-unaligned` | Do not output a file of unaligned sequences when using indel models. Default: a file `.unaligned.fa` containing unaligned sequences is written. |
-| `-q <PARTITION>` or <br>`-p <PARTITION>` or <br>`-Q <PARTITION>` | Specify different types of [Partition models](#partition-models)|
+| `-q <PARTITION>` or <br>`-p <PARTITION>` or <br>`-Q <PARTITION>` | Specify different types of [Partition models](#partition-models), i.e., edge-equal (-q), edge-proportional (-p), edge-unlinked (-Q)|
 | `--distribution <FILE>` | Supply a definition file of distributions, which could be used to generate random model parameters (see [Using user-defined parameter distributions](#using-user-defined-parameter-distributions)). |
 | `--branch-distribution <DISTRIBUTION>` | Specify a distribution, from which branch lengths of the input trees are randomly generated and overridden.|
 | `--branch-scale <SCALE>` | Specify a value to scale all branch lengths of the input tree.|