From f0fe3d37f6a6088ec962425ae892cf1880449d28 Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Wed, 20 Nov 2024 09:40:43 -0800
Subject: [PATCH] Use IQ-Tree

---
 phylogenetic/rules/construct_phylogeny.smk | 1 -
 1 file changed, 1 deletion(-)

diff --git a/phylogenetic/rules/construct_phylogeny.smk b/phylogenetic/rules/construct_phylogeny.smk
index 60da9a2..aa83f97 100644
--- a/phylogenetic/rules/construct_phylogeny.smk
+++ b/phylogenetic/rules/construct_phylogeny.smk
@@ -35,7 +35,6 @@ rule tree:
         augur tree \
             --alignment {input.alignment} \
             --output {output.tree} \
-            --method raxml \
             --nthreads {threads:q} 2>&1 | tee {log}
         """