Add option to set the starting index

Author: trongnhanuit

doc/AliSim.md

@@ -558,7 +558,7 @@ This example simulates a new alignment under the Juke-Cantor model from the inpu
 
 Pre-define mutations
 ----------------------------
-AliSim allows users to pre-define mutations that occur at some specific branches along the tree. To do so, one can specify those mutations via either a separate file or an input tree file.
+AliSim allows users to pre-define mutations that occur at some specific branches along the tree. Those mutations could be generated by running [VGsim](https://github.com/genomics-HSE/vgsim) with the option `-writeMutations`. One can specify those mutations via either a separate file (i.e., using the output file from VGsim) or an input tree file.
 
 ### Pre-define mutations via a separate file
 Given a tree file `tree_example.nwk`
@@ -575,6 +575,8 @@ Each line starts with a `<node name>`, followed by a tab `\t`, and ends up with
 * Three mutations `C39G` (i.e., C is substituted by G at site 39), `T17A`, and `G25C` occur along the branch connecting (the internal) node `I1` and its parent node (i.e., the root node);
 * Two mutations `C25A` and `A5G` occur along the branch connecting node `T2` and its parent node (i.e., node `I1').
 
+Note that, by default, the site indexes start from 0 (to make AliSim compatible with VGsim's output). One can add the option `--index-from-one` to set the site indexes start from 1.
+
 
 The following command