update funding and doc

Author: bqminh

_posts/news/2021-05-17-code-of-conduct.md

@@ -136,3 +136,4 @@ enforcement ladder](https://github.com/mozilla/diversity).
 For answers to common questions about this code of conduct, see the FAQ at
 <https://www.contributor-covenant.org/faq>. Translations are available at
 <https://www.contributor-covenant.org/translations>.
+

about.html

@@ -65,7 +65,14 @@ <h3>Credits </h3>
 
             <h3>Fundings</h3>
             <div class="hline"></div>
-                <p>Generous fundings for the IQ-TREE project are provided by the <a href="http://www.fwf.ac.at">Austrian Science Fund - FWF</a> (grants I 760-B17 from 2012-2015 and I 2508-B29 from 2016-2019) and the <a href="https://www.univie.ac.at">University of Vienna</a> (Initiativkolleg I059-N from 2011-2014).</p>
+                <p>Generous fundings for the IQ-TREE project are provided by the 
+                <a href="http://www.fwf.ac.at">Austrian Science Fund - FWF</a> 
+                (grants I 760-B17 from 2012-2015 and I 2508-B29 from 2016-2019),
+                 <a href="https://www.univie.ac.at">University of Vienna</a> 
+                 (Initiativkolleg I059-N from 2011-2014),
+                 <a href="https://www.arc.gov.au">Australian Research Council</a>
+                 Discovery Project (DP200103151),
+                 and <a href="https://chanzuckerberg.com">Chan-Zuckerberg Initiative</a> (EOSS-0000000132).</p>
 
         </div>
     </div><!--/row -->

doc/Advanced-Tutorial.md

@@ -2,7 +2,7 @@
 layout: userdoc
 title: "Advanced Tutorial"
 author: Jana, Minh Bui
-date:    2019-12-01
+date:    2021-05-19
 docid: 4
 icon: info-circle
 doctype: tutorial
@@ -196,7 +196,7 @@ IQ-TREE supports the partition-resampling strategy as suggested by ([Nei et al.,
 
 
 to resample partitions instead of sites. Moreover, IQ-TREE allows an even more complicated
-strategy: resampling partitions and then sites within resampled partitions  ([Gadagkar et al., 2005]). This may help to reduce false positives (i.e. wrong branch receiving 100% support):
+strategy: resampling partitions and then sites within resampled partitions  ([Gadagkar et al., 2005]; [Seo et al., 2005]). This may help to reduce false positives (i.e. wrong branch receiving 100% support):
 
 
     iqtree -s example.phy -p example.nex -B 1000 --sampling GENESITE
@@ -533,6 +533,7 @@ See [Command Reference](Command-Reference) for a complete list of all options av
 [Lanfear et al., 2014]: https://doi.org/10.1186/1471-2148-14-82
 [Lopez et al., 2002]: http://mbe.oxfordjournals.org/content/19/1/1.full
 [Nei et al., 2001]: https://doi.org/10.1073/pnas.051611498
+[Seo et al., 2005]: https://doi.org/10.1073/pnas.0408313102
 [Shimodaira and Hasegawa, 1999]: https://doi.org/10.1093/oxfordjournals.molbev.a026201
 [Shimodaira, 2002]: https://doi.org/10.1080/10635150290069913
 [Strimmer and Rambaut, 2002]: https://doi.org/10.1098/rspb.2001.1862

doc/Command-Reference.md

@@ -2,7 +2,7 @@
 layout: userdoc
 title: "Command Reference"
 author: Diep Thi Hoang, Dominik Schrempf, Heiko Schmidt, Jana Trifinopoulos, Minh Bui
-date:    2021-03-15
+date:    2021-05-19
 docid: 19
 icon: book
 doctype: manual
@@ -429,7 +429,7 @@ The ultrafast bootstrap (UFBoot) approximation ([Minh et al., 2013]; [Hoang et a
 | `-bcor`  | Specify minimum correlation coefficient for UFBoot convergence criterion. *DEFAULT: 0.99* |
 | `-beps`  | Specify a small epsilon to break tie in RELL evaluation for bootstrap trees. *DEFAULT: 0.5* |
 | `-bnni` | Perform an additional step to further optimize UFBoot trees by nearest neighbor interchange (NNI) based directly on bootstrap alignments. This option is recommended in the presence of **severe model violations**. It increases computing time by 2-fold but reduces the risk of overestimating branch supports due to severe model violations. Introduced in IQ-TREE 1.6. |
-| `-bsam` | Specify the resampling strategies for partitioned analysis. By default, IQ-TREE resamples alignment sites within partitions. With `-bsam GENE` IQ-TREE will resample partitions. With `-bsam GENESITE` IQ-TREE will resample partitions and then resample sites within resampled partitions ([Gadagkar et al., 2005]). |
+| `-bsam` | Specify the resampling strategies for partitioned analysis. By default, IQ-TREE resamples alignment sites within partitions. With `-bsam GENE` IQ-TREE will resample partitions. With `-bsam GENESITE` IQ-TREE will resample partitions and then resample sites within resampled partitions ([Gadagkar et al., 2005]; [Seo et al., 2005]). |
 | `-nm`    | Specify maximum number of iterations to stop. *DEFAULT: 1000* |
 | `-nstep` | Specify iteration interval checking for UFBoot convergence. *DEFAULT: every 100 iterations* |
 | `-wbt`   | Turn on writing bootstrap trees to `.ufboot` file. *DEFAULT: OFF* |
@@ -729,6 +729,7 @@ The first few lines of the output file example.phy.sitelh (printed by `-wslr` op
 [Lartillot and Philippe, 2004]: https://doi.org/10.1093/molbev/msh112
 [Minh et al., 2013]: https://doi.org/10.1093/molbev/mst024
 [Nguyen et al., 2015]: https://doi.org/10.1093/molbev/msu300
+[Seo et al., 2005]: https://doi.org/10.1073/pnas.0408313102
 [Shimodaira and Hasegawa, 1999]: https://doi.org/10.1093/oxfordjournals.molbev.a026201
 [Shimodaira, 2002]: https://doi.org/10.1080/10635150290069913
 [Soubrier et al., 2012]: https://doi.org/10.1093/molbev/mss140

doc/Rootstrap.md

@@ -1,8 +1,8 @@
 ---
 layout: userdoc
 title: "Rooting phylogenies"
-author: 152suha, Minh Bui
-date:    2021-04-21
+author: Minh Bui, Suha Naser
+date:    2021-05-18
 docid: 8
 icon: info-circle
 doctype: tutorial
@@ -108,7 +108,7 @@ as the run above to infer an unrooted tree using reversible models:
 This run will also write the best partitioning scheme to `rev_dna.best_scheme.nex` file.
 In the second step, we will re-use this best scheme but replace the substitution model 
 with the most general non-reversible DNA model, 12.12 or UNREST 
-(see [this doc]((Substitution-Models#lie-markov-models))) to obtain a rooted tree:
+(see [this doc](Substitution-Models#lie-markov-models)) to obtain a rooted tree:
 
     iqtree2 -s bovidae.phy -p rev_dna.best_scheme.nex --model-joint 12.12 -B 1000 -T AUTO --prefix nonrev_dna
 

doc/convertwiki.sh

@@ -31,7 +31,7 @@ for f in *.md workshop/*.md; do
 
     let file_changed++
 
-    AUTHOR=`git log $f | grep Author: | sed 's/m.bui@anu/minh.bui@anu/' | sed 's/.* <//' | sed 's/@.*//' | sed 's/\./ /g' | sort | uniq | tr '\n' ',' | sed 's/,$//' | sed 's/,/, /g' | awk '{for(i=1;i<=NF;i++){ $i=toupper(substr($i,1,1)) substr($i,2) }}1'`
+    AUTHOR=`git log $f | grep Author: | sed 's/m.bui@anu/minh.bui@anu/' | sed 's/152suha/suha.naser/' | sed 's/.* <//' | sed 's/@.*//' | sed 's/\./ /g' | sort | uniq | tr '\n' ',' | sed 's/,$//' | sed 's/,/, /g' | awk '{for(i=1;i<=NF;i++){ $i=toupper(substr($i,1,1)) substr($i,2) }}1'`
     DATE=`git log --date=short $f | grep Date: | head -n 1 | sed 's/Date://'`
 
     sed "s/_AUTHOR_/$AUTHOR/" $f | sed "s/_DATE_/$DATE/" | sed 's/\.\.\//\.\.\/doc\//g'  > $destf

doc/iqtree-doc.pdf

@@ -81,8 +81,8 @@ <h3>COVID-19 release {{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>
+                    May 17, 2021: We published a <a href="news/code-of-conduct">Code of Conduct</a> for the IQ-TREE community<br>
+                    April 21, 2021: <a href="doc/Rootstrap">Rooting phylogenies and Rootstrap measure</a> is now available in v2.1.3<br>
                 </div>
             </div>
         </div>

index.html

@@ -1,7 +1,7 @@
 ---
 layout: workshop
 title: "Workshop"
-date:    2021-05-17
+date:    2019-08-01
 ---
 
 Throughout the year, members of IQ-TREE development team teach workshops on molecular evolution, phylogenetics, phylogenomics, and maximum likelihood using IQ-TREE.
@@ -11,7 +11,8 @@ Throughout the year, members of IQ-TREE development team teach workshops on mole
 
 | Date |  Course Title | Location | Instructor |
 |------|---------------|----------------------------|-------------|
-| late July, 2021 | Phylogenetic Analysis with IQ-TREE | [Sydney Phylogenetics Workshop](https://meep.sydney.edu.au/workshops/), virtual workshop | Bui Quang Minh |
+| Aug 1-11, 2019 | [IQ-TREE Workshop Tutorial](molevol2019) | [Workshop on Molecular Evolution](https://molevol.mbl.edu), Marine Biological Laboratory, Woods Hole, USA | Bui Quang Minh |
+| Aug 4-9, 2019 | Several sessions | [Workshop on Virus Evolution and Molecular Epidemiology](https://rega.kuleuven.be/cev/veme-workshop/2019), The University of Hong Kong, Hong Kong | Heiko Schmidt |
 
 
 ### Past Workshops
@@ -20,9 +21,6 @@ IQ-TREE was taught as part of the following workshops:
 
 | Date |  Course Title | Location | Instructor |
 |------|---------------|----------------------------|-------------|
-| Jan 28-29, 2021 | Phylogenetic Analysis with IQ-TREE | [Sydney Phylogenetics Workshop](https://meep.sydney.edu.au/workshops/), virtual workshop | Bui Quang Minh |
-| Aug 1-11, 2019 | [IQ-TREE Workshop Tutorial](molevol2019) | [Workshop on Molecular Evolution](https://molevol.mbl.edu), Marine Biological Laboratory, Woods Hole, USA | Bui Quang Minh |
-| Aug 4-9, 2019 | Several sessions | [Workshop on Virus Evolution and Molecular Epidemiology](https://rega.kuleuven.be/cev/veme-workshop/2019), The University of Hong Kong, Hong Kong | Heiko Schmidt |
 | Jan 24, 2019 | [IQ-TREE intro and lab](ck2019) | [Workshop on Phylogenomics](http://evomics.org/workshops/2019-workshop-on-phylogenomics-cesky-krumlov/), Cesky Krumlov, Czech Republic | Stephen Crotty |
 | Dec 7, 2018 | [Phylogenomics using IQ-TREE](anu2018) | [Phylogenomics Workshop using IQ-TREE](http://cba.anu.edu.au/news-events/phylogenomics-workshop-using-iq-tree), Australian National University, Canberra, Australia | Rob Lanfear, Minh Bui |
 | Aug 26, 2018 | ML Phylogenetics and IQ-TREE | [Workshop on Virus Evolution and Molecular Epidemiology](https://rega.kuleuven.be/cev/veme-workshop/2018), Robert Koch-Institut, Berlin, Germany | Heiko Schmidt |