update concordance paper and blmin option

bqminh · bqminh · commit e0f53144e2e2 · 2020-05-08T12:46:18.000+10:00
diff --git a/_data/pubdata.yml b/_data/pubdata.yml
@@ -27,11 +27,38 @@ references:
   title-short: IQ-TREE 2
   container-title: Mol. Biol. Evol.
   publisher: Oxford University Press
-  issue: in press
+  page: '1530-1534'
+  volume: '37'
+  issue: '5'
   DOI: 10.1093/molbev/msaa015
   message: General citation for IQ-TREE 2&#58;
   new: yes
 
+- author:
+  - family: Minh
+    given: B.Q.
+  - family: Hahn
+    given: M.W.
+  - family: Lanfear
+    given: R.
+  editor:
+  - family: Rosenberg
+    given: Michael
+  issued:
+    year: 2020
+    month: 5
+  accessed:
+  - year: 2020
+    month: 5
+    day: 7
+  title: New methods to calculate concordance factors for phylogenomic datasets
+  container-title: Mol. Biol. Evol.
+  page: in press
+  DOI: 10.1093/molbev/msaa106
+  message: When using <a href="doc/Concordance-Factor">concordance factors</a> please cite&#58;
+  new: yes
+
+
 - author:
   - given: S.M.
     family: Crotty
@@ -50,7 +77,7 @@ references:
   - given: A.
     family: von Haeseler
   issued:
-    year: 2019
+    year: 2020
     month:
   title: "GHOST: Recovering historical signal from heterotachously-evolved sequence alignments"
   container-title: Syst. Biol.
@@ -132,12 +159,12 @@ references:
     month:
   title: Polymorphism-aware species trees with advanced mutation models, bootstrap, and rate heterogeneity
   container-title: Mol. Biol. Evol.
-  issue: 36
+  volume: 36
+  issue: 6
   page: 1294–1301
   DOI: 10.1093/molbev/msz043
   software: http://www.iqtree.org/
   message: When using <a href="doc/Polymorphism-Aware-Models">polymorphism-aware models</a> please cite&#58;
-  new: yes
 
 - author:
   - given: D.T.
@@ -160,7 +187,8 @@ references:
   title: UFBoot2&#58; Improving the ultrafast bootstrap approximation
   container-title: Mol. Biol. Evol.
   publisher: Oxford University Press
-  issue: 35
+  volume: 35
+  issue: 2
   page: 518–522
   DOI: 10.1093/molbev/msx281
   type: article-journal
@@ -183,7 +211,8 @@ references:
   title: Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation
   container-title: Syst. Biol.
   publisher: Oxford University Press
-  issue: 67
+  volume: 67
+  issue: 2
   page: 216–235
   DOI: 10.1093/sysbio/syx068
   PMID: 28950365
@@ -210,7 +239,7 @@ references:
   DOI: 10.1038/nmeth.4285
   PMID: 28481363
   PMCID: PMC5453245
-  issue: 14
+  volume: 14
   page: 587-589
   software: http://www.iqtree.org/
   message: When using <a href="doc/Tutorial#choosing-the-right-substitution-model">model selection (ModelFinder)</a> please cite&#58;
@@ -226,7 +255,8 @@ references:
     year: 2016
   title: Terrace aware data structure for phylogenomic inference from supermatrices
   container-title: Syst. Biol.
-  issue: 65
+  volume: 65
+  issue: 6
   page: 997-1008
   DOI: 10.1093/sysbio/syw037
   PMID: 27121966
@@ -246,7 +276,8 @@ references:
     year: 2016
   title: W-IQ-TREE&#58; a fast online phylogenetic tool for maximum likelihood analysis.
   container-title: Nucleic Acids Res.
-  issue: 44
+  volume: 44
+  issue: W1
   page: W232-W235
   DOI: 10.1093/nar/gkw256
   PMID: 27084950
@@ -266,7 +297,8 @@ references:
     year: 2015
   title: IQ-TREE&#58; A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.
   container-title: Mol. Biol. Evol.
-  issue: 32
+  volume: 32
+  issue: 1
   page: 268-274
   DOI: 10.1093/molbev/msu300
   PMID: 25371430
diff --git a/doc/Command-Reference.md b/doc/Command-Reference.md
@@ -2,7 +2,7 @@
 layout: userdoc
 title: "Command Reference"
 author: Diep Thi Hoang, Dominik Schrempf, Heiko Schmidt, Jana Trifinopoulos, M Bui, Minh Bui
-date:    2018-11-29
+date:    2020-04-24
 docid: 7
 icon: book
 doctype: tutorial
@@ -640,7 +640,7 @@ Miscellaneous options
 |-----------|------------------------------------------------------------------------------|
 | `-alninfo` | Print alignment site statistics to `.alninfo` file. |
 | `-blfix`   | Fix branch lengths of tree passed via `-t` or `-te`. This is useful to evaluate the log-likelihood of an input tree with fixed tolopogy and branch lengths. *DEFAULT: OFF* |
-| `-blmin`  | Specify minimum branch length. Default: the smaller of 0.000001 and alignment length divided by 10. |
+| `-blmin`  | Specify minimum branch length. Default: the smaller of 0.000001 and 0.1/alignment_length. |
 | `-blmax`  | Specify the maximum branch length. Default: 10 |
 | `-czb`    | Collapse near zero branches, so that the final tree may be multifurcating. This is useful for bootstrapping in the presence of polytomy to reduce bootstrap supports of short branches. |
 | `-me`      | Specify the log-likelihood epsilon for final model parameter estimation (Default: 0.01). With `-fast` option, the epsilon is raised to 0.05. | 
diff --git a/doc/Concordance-Factor.md b/doc/Concordance-Factor.md
@@ -2,8 +2,8 @@
 layout: userdoc
 title: "Concordance Factor"
 author: M Bui
-date:    2019-12-01
-docid: 6
+date:    2020-05-08
+docid: 5
 icon: info-circle
 doctype: tutorial
 tags:
@@ -28,7 +28,9 @@ Concordance Factor
 
 Since IQ-TREE 2, we provide two measures for quantifying genealogical concordance in phylogenomic datasets: the gene concordance factor (gCF) and the site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of “decisive” gene trees containing that branch. gCF is already in wide usage, but here we allow to calculate gCF while correctly accounting for variable taxon coverage among the gene trees. sCF is defined as the percentage of decisive alignment sites supporting a branch in the reference tree. sCF is a novel measure that is particularly useful when individual gene alignments are relatively uninformative, such that gene trees are uncertain. gCF and sCF complement classical measures of branch support (e.g. bootstrap) in phylogenetics by providing a full description of underlying disagreement among loci and sites.
 
-If you use this feature please cite: __Minh B.Q., Hahn M., Lanfear R.__ (2018) New methods to calculate concordance factors for phylogenomic datasets. <https://doi.org/10.1101/487801>
+If you use this feature please cite: 
+
+__Minh B.Q., Hahn M.W., Lanfear R.__ (2020) New methods to calculate concordance factors for phylogenomic datasets. _Molecular Biology and Evolution_, in press. <https://doi.org/10.1093/molbev/msaa106>
 
 >**NOTE**: For this feature please use IQ-TREE version 2!
 
diff --git a/doc/Front.md b/doc/Front.md
@@ -6,7 +6,7 @@ title: |
     
 subtitle: "<http://www.iqtree.org>"
 author: Bui Quang Minh, Jana Trifinopoulos, Dominik Schrempf, Heiko A. Schmidt
-date: December 1, 2019
+date: April 27, 2020
 keywords: [phylogenomic inference, maximum likelihood]
 toc: true
 papersize: A4
diff --git a/doc/convertwiki.sh b/doc/convertwiki.sh
@@ -12,7 +12,7 @@ cd $source_dir
 
 file_changed=0
 
-files="Front.md Home.md Quickstart.md Web-Server-Tutorial.md Tutorial.md Advanced-Tutorial.md Concordance-Factor.md Command-Reference.md Substitution-Models.md Complex-Models.md Polymorphism-Aware-Models.md Compilation-Guide.md Frequently-Asked-Questions.md"
+files="Front.md Home.md Quickstart.md Web-Server-Tutorial.md Tutorial.md Advanced-Tutorial.md Concordance-Factor.md Dating.md Command-Reference.md Substitution-Models.md Complex-Models.md Polymorphism-Aware-Models.md Compilation-Guide.md Frequently-Asked-Questions.md"
 
 for f in *.md workshop/*.md; do
     if [ "$f" == "_Footer.md" -o "$f" == "_Sidebar.md" ]; then
diff --git a/doc/iqtree-doc.pdf b/doc/iqtree-doc.pdf
diff --git a/index.html b/index.html
@@ -3,9 +3,9 @@
 title: "IQ-TREE: Efficient phylogenomic software by maximum likelihood"
 permalink: /
 version: 1.6.12
-version_new: 2.0-rc2
+version_new: 2.0.4
 releasedate: August 15, 2019
-releasedate_new: March 28, 2020
+releasedate_new: April 27, 2020
 ---
 <!-- ========================== HEADER ========================== -->
 <div id="headerwrap">
@@ -79,6 +79,7 @@ <h3>Release candidate {{page.version_new}} ({{page.releasedate_new}})</h3>
             <div class="list-group">
                 <div class="list-group-item list-group-item-success">
                     <h4 class="centered">LATEST NEWS</h4>
+                    April 24, 2020: <a href="doc/Dating">Phylogenetic dating</a> is now available in v2.0.3.<br>
                     One <a href="news/phd-position">PhD position</a> and one software engineer available. Please contact m.bui (-a-) anu.edu.au<br>
                 </div>
             </div>
@@ -306,7 +307,7 @@ <H4>{{pub.message}}
 		        	{% endfor %}
 		        </strong> 
 		        ({{pub.issued.year}}) {{pub.title}}.
-		        <EM>{{pub.container-title}}</EM>{% if pub.issue %}, {{pub.issue}}:{{pub.page}}. {% endif %}
+		        <EM>{{pub.container-title}}</EM>{% if pub.volume %}, {{pub.volume}}:{{pub.page}}. {% endif %}
 		        <A href="https://doi.org/{{pub.DOI}}">https://doi.org/{{pub.DOI}}</A>
 		    </div><!--col-->
 	        <div class="col-xs-2  col-md-1">
