From 90371668c2f0945495f220cdfe76a5a743036ba8 Mon Sep 17 00:00:00 2001
From: Weiwen Wang <u4987172@anu.edu.au>
Date: Tue, 6 Dec 2022 18:13:02 +0800
Subject: [PATCH] Update Running_DecentTree.md

---
 doco/Running_DecentTree.md | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/doco/Running_DecentTree.md b/doco/Running_DecentTree.md
index 09c1efa..ccb7ff2 100644
--- a/doco/Running_DecentTree.md
+++ b/doco/Running_DecentTree.md
@@ -1,4 +1,19 @@
 <h1>Running decenttree</h1>
+
+This is an example of how to run decenttree with Neighbor Joining algorithm. Other algorithms can be found in https://github.com/iqtree/decenttree/blob/master/doco/Algorithms.md.
+
+If the input file is in multiple sequence alignment format (.fasta, can be compressed)
+
+```
+decentTree -fasta $inputFile -t NJ -out $outputFile
+```
+
+If the input file is in distance matrix format
+
+```
+decentTree -in $inputFile -t NJ -out $outputFile
+```
+
 <h2>Command-line options</h2>
 
 | Option      | Argument               | Description |