From dbd102a38662f6d2337f40b0064e26c6a6b3d3b0 Mon Sep 17 00:00:00 2001
From: Thomas Wong <thomaskf@gmail.com>
Date: Thu, 18 Apr 2024 14:01:31 +1000
Subject: [PATCH] update the extension of the outputted nex file for linked GTR
 model

---
 main/phyloanalysis.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/main/phyloanalysis.cpp b/main/phyloanalysis.cpp
index 8665f3e88..17c176cac 100644
--- a/main/phyloanalysis.cpp
+++ b/main/phyloanalysis.cpp
@@ -1154,7 +1154,7 @@ void printOutfilesInfo(Params &params, IQTree &tree) {
     }
     
     if (params.optimize_linked_gtr) {
-        cout << "  GTRPMIX nex file:              " << params.out_prefix << ".gtrpmix.nex" << endl;
+        cout << "  GTRPMIX nex file:              " << params.out_prefix << ".GTRPMIX.nex" << endl;
     }
     cout << endl;
 
@@ -1834,7 +1834,7 @@ void reportPhyloAnalysis(Params &params, IQTree &tree, ModelCheckpoint &model_in
             ModelSubst *mmodel = tree.getModel();
             ModelMarkov *m = (ModelMarkov*)mmodel->getMixtureClass(0);
             string outnexfile = params.out_prefix;
-            outnexfile += ".gtrpmix.nex";
+            outnexfile += ".GTRPMIX.nex";
             ofstream outnex;
             outnex.exceptions(ios::failbit | ios::badbit);
             outnex.open(outnexfile.c_str());