From 644a4a4963fdedb9d4a9716f8971b6216168b99c Mon Sep 17 00:00:00 2001
From: Sina Majidian <sina.majidian@gmail.com>
Date: Wed, 20 Dec 2023 08:27:32 +0100
Subject: [PATCH] bootstraping & DNA-mode

---
 README.md | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/README.md b/README.md
index 86f46f3..cf479e1 100644
--- a/README.md
+++ b/README.md
@@ -112,6 +112,23 @@ read2tree --standalone_path marker_genes/ --output_path output --reads species3_
 read2tree --standalone_path marker_genes/ --output_path output --merge_all_mappings --tree
 ```
 
+### bootstraping
+
+To have bootstrap values a metric for quality of internal nodes, you can run the following 
+```
+thread=20
+iqtree -T ${thread} -s output/concat_*_aa.phy  -bb 1000 
+```
+The `.phy` file is either `concat_sample_aa.phy` or `concat_merge_aa.phy` corresponding to single- or multi-species mode. 
+
+It is also possible to us [trimal](http://trimal.cgenomics.org/use_of_the_command_line_trimal_v1.2) for trimming msa `trimal -in <inputfile> -out <outputfile> -automated1` 
+
+### DNA-mode tree inferrence
+For closely related species, the user can infer tree using MSA of nucleotide sequences. 
+```
+thread=20
+iqtree -T ${thread} -s output/concat_*_dna.phy 
+```
 
 ## Test example