From 231c8c3123bd12e52b21f95eacf3eaab7068ab51 Mon Sep 17 00:00:00 2001 From: Bui Quang Minh Date: Thu, 18 Jun 2026 09:19:05 +1000 Subject: [PATCH] Update maximum-likelihood tree models in Quickstart Updated model descriptions and added new model for protein alignment. --- doc/Quickstart.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/doc/Quickstart.md b/doc/Quickstart.md index 433f0c0..3de8362 100644 --- a/doc/Quickstart.md +++ b/doc/Quickstart.md @@ -122,9 +122,13 @@ A few typically analyses are listed in the following. Note that it is assumed th iqtree -s example.phy -* Infer maximum-likelihood tree using `GTR+I+G` model: +* Infer maximum-likelihood tree using `GTR+I+R` model for DNA alignment: - iqtree -s example.phy -m GTR+I+G + iqtree -s example.phy -m GTR+I+R + +* Infer maximum-likelihood tree using `QC.PFAM+F+I+R` model for protein alignment: + + iqtree -s prot.phy -m QC.PFAM+F+I+R * Perform ModelFinder without subsequent tree inference: