From d353cc0b47d956516b15f4cae2fa2fd5519aab65 Mon Sep 17 00:00:00 2001
From: Benjamin Redelings <benjamin.redelings@gmail.com>
Date: Mon, 30 Dec 2024 20:19:43 -0800
Subject: [PATCH] Mention MNM mutation models.

---
 NEWS                          | 3 ++-
 bindings/models/busted.json   | 7 ++++---
 bindings/models/busted_s.json | 3 ++-
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/NEWS b/NEWS
index c4bf5e00f..2396bfc01 100644
--- a/NEWS
+++ b/NEWS
@@ -1,6 +1,7 @@
 * 4.0-beta17 (unreleased)
 - Models:
-  + multi-nucleotide-mutation (mnm) model for codons.
+  + Multi-Nucleotide-Mutation (MNM) model for codons.
+  + BUSTED and BUSTED-S substitution models for positive selection.
 - Bug fixes:
  + Log sorted (conserved) omegas in m3_test.
 
diff --git a/bindings/models/busted.json b/bindings/models/busted.json
index 006a68159..32a542569 100644
--- a/bindings/models/busted.json
+++ b/bindings/models/busted.json
@@ -41,7 +41,7 @@
 	    "description": "The number of conserved omega categories, if not specified"
         }
     ],
-    "description": "This model performs a Bayesian test of positive selection using the BUSTED model.  Instead of using a covarion process, the BUSTED model simply lets each (branch,site) pair choose a rate matrix from a mixture of `n` conserved rates matrices and 1 positively-selected rate matrix.\nThe test for positive selection compares the unrestricted BUSTED model to a restricted version with posW=1.  The posterior probability that posSelection=1 is posterior probability for positive selection.\nAll branches are treated as foreground branches.",
+    "description": "This model performs a Bayesian test of positive selection using the BUSTED model.  The BUSTED model constructs a weighted list of (n+1) dN/dS values and constructs rate matrices from them.  The first n rate matrices are conserved, and the last rate matrix is positive selected with weight posP and dNdS=posW. Instead switching between these rate matrices using a covarion process, the BUSTED model simply lets each (branch,site) pair choose a rate matrix from the mixture.\nThe test for positive selection compares the unrestricted BUSTED model to a restricted version with posW=1.  The posterior probability that posSelection=1 is posterior probability for positive selection.\nAll branches are treated as foreground branches.",
     "extract": "all",
     "citation": {"type": "article",
 		 "title": "Gene-Wide Identification of Episodic Selection",
@@ -62,8 +62,9 @@
 		 "journal": {"name": "Mol. Biol. Evol.", "volume": "32", "number": "5", "pages": "1365--1371"},
 		 "link": [{"url":"https://doi.org/10.1093/molbev/msv035"}]
 		},
-    "examples": ["busted +> Rates.gamma    // This is the same as BUSTED-S",
+    "examples": ["busted +> Rates.gamma(n=3)                              // with synonymous rate variation (= BUSTED-S)",
 		 "busted +> Rates.free",
-		 "|w: gtr +> x3 +> dNdS(omega=w) +> mut_sel| +> busted"],
+		 "|w: gtr +> mnm +> dNdS(omega=w)| +> busted              // with multi-nucleotide mutations",
+		 "|w: gtr +> x3 +> dNdS(omega=w) +> mut_sel| +> busted    // with mutation-selection-balance"],
     "see": ["busted_s"]
 }
diff --git a/bindings/models/busted_s.json b/bindings/models/busted_s.json
index f4b844224..b57cbc876 100644
--- a/bindings/models/busted_s.json
+++ b/bindings/models/busted_s.json
@@ -66,5 +66,6 @@
 		 "link": [{"url":"https://doi.org/10.1093/molbev/msaa037"}]
 		},
     "see": ["busted"],
-    "examples": ["|w: tn93 +> x3 +> dNdS(omega=w)| +> busted_s"]
+    "examples": ["|w: tn93 +> x3 +> dNdS(omega=w)| +> busted_s",
+		 "|w: tn93 +> mnm +> dNdS(omega=w)| +> busted_s"]
 }