From 1fb406a74c4ba0a5b390f8cbf7157e9868c4a1a8 Mon Sep 17 00:00:00 2001
From: JLSteenwyk <jlsteenwyk@gmail.com>
Date: Thu, 12 Sep 2024 12:56:33 -0700
Subject: [PATCH] updated change logs to reflect new partition file generated
 from the create_concat function

---
 change_log.txt            |  9 +++++++++
 docs/change_log/index.rst |  8 ++++++++
 phykit/phykit.py          | 10 +++++-----
 3 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/change_log.txt b/change_log.txt
index a32b44a..894f56f 100644
--- a/change_log.txt
+++ b/change_log.txt
@@ -1,5 +1,14 @@
 Major changes to PhyKIT are summarized here.
 
+1.21.0
+  - The partition file outputted from the create_concat function has been updated
+  - Column information in the partition file is as follows:
+    - column 1: alignment name
+    - column 2: # of taxa present
+    - column 3: # of taxa missing
+    - column 4: fraction of occupancy
+    - column 5: names of missing taxa (; separated)
+
 1.20.0
   - Fixed bug for thread_dna function when using a ClipKIT log file. Input protein alignment must be the untrimmed alignment.
 
diff --git a/docs/change_log/index.rst b/docs/change_log/index.rst
index 0e4318d..5585d84 100644
--- a/docs/change_log/index.rst
+++ b/docs/change_log/index.rst
@@ -8,6 +8,14 @@ Change log
 
 Major changes to PhyKIT are summarized here.
 
+**1.21.0**:
+The partition file outputted from the create_concat function has been updated to the following format:
+- column 1: alignment name
+- column 2: # of taxa present
+- column 3: # of taxa missing
+- column 4: fraction of occupancy
+- column 5: names of missing taxa (; separated)
+
 **1.20.0**:
 Fixed bug for thread_dna function when using a ClipKIT log file. Input protein alignment must be the untrimmed alignment.
 
diff --git a/phykit/phykit.py b/phykit/phykit.py
index ed8528b..1500b4f 100644
--- a/phykit/phykit.py
+++ b/phykit/phykit.py
@@ -2563,11 +2563,11 @@ def create_concatenation_matrix(argv):
                 2) A partition file ready for input into RAxML or IQ-tree.
                 3) An occupancy file that summarizes the taxon occupancy
                    per sequence.
-                   - column 1: alignment name
-                   - column 2: # of taxa present
-                   - column 3: # of taxa missing
-                   - column 4: # fraction of occupancy
-                   - column 5: # names of missing taxa (; separated)
+                        - column 1: alignment name
+                        - column 2: # of taxa present
+                        - column 3: # of taxa missing
+                        - column 4: fraction of occupancy
+                        - column 5: names of missing taxa (; separated)
 
                 Aliases:
                   create_concatenation_matrix, create_concat, cc