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JLSteenwyk · Jun 23, 2023 · f914c5f · f914c5f
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diff --git a/_sources/change_log/index.rst.txt b/_sources/change_log/index.rst.txt
@@ -9,4 +9,7 @@ Change log
 Major changes to OrthoSNAP are summarized here.
 
 **0.1.0**
-Added -r/\-\-rooted, -st/\-\-snap_trees, and -ip/\-\-inparalog_to_keep functions
+Added -r/\-\-rooted, -st/\-\-snap_trees, and -ip/\-\-inparalog_to_keep functions
+
+**1.0.0**
+Improved species inparalog pruning
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
@@ -10,10 +10,10 @@ can then be used for diverse studies including phylogenomics and genome-wide sur
 selection.
 
 If you found OrthoSNAP useful, please cite *OrthoSNAP: a tree splitting and pruning algorithm
-for retrieving single-copy orthologs from gene family trees*. bioRxiv. doi: |doiLink|_.
+for retrieving single-copy orthologs from gene family trees*. PLOS Biology. doi: |doiLink|_.
 
-.. _doiLink: https://www.biorxiv.org/content/10.1101/2021.10.30.466607v1
-.. |doiLink| replace:: 10.1101/2021.10.30.466607
+.. _doiLink: https://jlsteenwyk.com/publication_pdfs/2022_Steenwyk_etal_PLoS_Biology.pdf
+.. |doiLink| replace:: 10.1371/journal.pbio.3001827
 
 |
 

diff --git a/change_log/index.html b/change_log/index.html
@@ -162,6 +162,8 @@
 <p>Major changes to OrthoSNAP are summarized here.</p>
 <p><strong>0.1.0</strong>
 Added -r/--rooted, -st/--snap_trees, and -ip/--inparalog_to_keep functions</p>
+<p><strong>1.0.0</strong>
+Improved species inparalog pruning</p>
 </div>
 
 

diff --git a/index.html b/index.html
@@ -161,7 +161,7 @@
 can then be used for diverse studies including phylogenomics and genome-wide surveys of positive
 selection.</p>
 <p>If you found OrthoSNAP useful, please cite <em>OrthoSNAP: a tree splitting and pruning algorithm
-for retrieving single-copy orthologs from gene family trees</em>. bioRxiv. doi: <a class="reference external" href="https://www.biorxiv.org/content/10.1101/2021.10.30.466607v1">10.1101/2021.10.30.466607</a>.</p>
+for retrieving single-copy orthologs from gene family trees</em>. PLOS Biology. doi: <a class="reference external" href="https://jlsteenwyk.com/publication_pdfs/2022_Steenwyk_etal_PLoS_Biology.pdf">10.1371/journal.pbio.3001827</a>.</p>
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diff --git a/searchindex.js b/searchindex.js