Update citation info

README.md

@@ -9,19 +9,20 @@ Rails 5 source for the [Iroki webapp](https://www.iroki.net), a viewer and custo
 If you find Iroki useful in your research, please cite the (updated) [Iroki preprint](https://doi.org/10.1101/106138).  Thank you!!
 
 ```
-Moore RM, Harrison AO, McAllister SM, and Wommack KE.  Iroki: automatic customization and visualization of phylogenetic trees.  bioRxiv 106138 (2018). doi:10.1101/106138
+Moore RM, Harrison AO, McAllister SM, Polson SW, and Wommack KE.  Iroki: automatic customization and visualization of phylogenetic trees.  bioRxiv 106138 (2019). doi:10.1101/106138
 ```
 
 You can also download the citation and import it into your favorite reference manager!
 
 - [BibTeX](https://raw.githubusercontent.com/mooreryan/iroki/master/manuscript_citation/iroki_-automatic-customization-and-visualization-of-phylogenetic-trees.bib)
 - [EndNote (tagged)](https://raw.githubusercontent.com/mooreryan/iroki/master/manuscript_citation/iroki_-automatic-customization-and-visualization-of-phylogenetic-trees.enw)
 - [EndNote 8 (xml)](https://raw.githubusercontent.com/mooreryan/iroki/master/manuscript_citation/iroki_-automatic-customization-and-visualization-of-phylogenetic-trees.xml)
+- [Refworks (tagged)](https://raw.githubusercontent.com/mooreryan/iroki/master/manuscript_citation/iroki_-automatic-customization-and-visualization-of-phylogenetic-trees.txt)
 - [RIS | Zotero | Mendeley](https://raw.githubusercontent.com/mooreryan/iroki/master/manuscript_citation/iroki_-automatic-customization-and-visualization-of-phylogenetic-trees.ris)
 
 ### Manuscript
 
-In addition to viewing the [manuscript on bioRxiv](https://doi.org/10.1101/106138), we have included a copy of the pdf [here](https://github.com/mooreryan/iroki/blob/master/manuscript_citation/iroki_-automatic-customization-and-visualization-of-phylogenetic-trees.pdf).
+Check out the [manuscript on bioRxiv](https://doi.org/10.1101/106138)!
 
 ## Documentation
 

app/views/layouts/_citation.html.slim

@@ -1,3 +1,3 @@
-p If you find Iroki useful in your research, please cite the Iroki #{link_to "preprint", "https://www.biorxiv.org/content/early/2018/08/15/106138"}.  Thank you!!
+p If you find Iroki useful in your research, please cite the Iroki #{link_to "preprint", "https://doi.org/10.1101/106138"}.  Thank you!!
 
-blockquote Moore RM, Harrison AO, McAllister SM, and Wommack KE.  Iroki: automatic customization and visualization of phylogenetic trees.  bioRxiv 106138 (2018). doi:10.1101/106138
+blockquote Moore RM, Harrison AO, McAllister SM, Polson SW, and Wommack KE.  Iroki: automatic customization and visualization of phylogenetic trees.  bioRxiv 106138 (2019). doi:10.1101/106138

manuscript_citation/iroki_-automatic-customization-and-visualization-of-phylogenetic-trees.bib

@@ -1,11 +1,12 @@
 @article {Moore106138,
-	author = {Moore, Ryan M and Harrison, Amelia O and McAllister, Sean M and Wommack, K. Eric},
+	author = {Moore, Ryan M. and Harrison, Amelia O. and McAllister, Sean M. and Polson, Shawn W. and Wommack, K. Eric},
 	title = {Iroki: automatic customization and visualization of phylogenetic trees},
-	year = {2018},
+	elocation-id = {106138},
+	year = {2019},
 	doi = {10.1101/106138},
 	publisher = {Cold Spring Harbor Laboratory},
-	abstract = {Phylogenetic trees are an important analytical tool for examining community diversity and the evolutionary history of species. In the case of microorganisms, decreasing sequencing costs have enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets present challenges to the extraction of meaningful trends from complex trees. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. To address these issues, we developed Iroki, a user-friendly web interface for tree visualization that provides automatic customization of phylogenetic trees based on metadata and abundance information. The Iroki web app and documentation is available at http://www.iroki.net or through the VIROME portal (http://virome.dbi.udel.edu). Iroki{\textquoteright}s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.},
-	URL = {https://www.biorxiv.org/content/early/2018/08/15/106138},
-	eprint = {https://www.biorxiv.org/content/early/2018/08/15/106138.full.pdf},
+	abstract = {Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki{\textquoteright}s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal (http://virome.dbi.udel.edu). Iroki{\textquoteright}s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.},
+	URL = {https://www.biorxiv.org/content/early/2019/09/28/106138},
+	eprint = {https://www.biorxiv.org/content/early/2019/09/28/106138.full.pdf},
 	journal = {bioRxiv}
 }

manuscript_citation/iroki_-automatic-customization-and-visualization-of-phylogenetic-trees.enw

@@ -1,12 +1,14 @@
 %0 Journal Article
-%A Moore, Ryan M
-%A Harrison, Amelia O
-%A McAllister, Sean M
+%A Moore, Ryan M.
+%A Harrison, Amelia O.
+%A McAllister, Sean M.
+%A Polson, Shawn W.
 %A Wommack, K. Eric
 %T Iroki: automatic customization and visualization of phylogenetic trees
-%D 2018
+%D 2019
 %R 10.1101/106138
 %J bioRxiv
-%X Phylogenetic trees are an important analytical tool for examining community diversity and the evolutionary history of species. In the case of microorganisms, decreasing sequencing costs have enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets present challenges to the extraction of meaningful trends from complex trees. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. To address these issues, we developed Iroki, a user-friendly web interface for tree visualization that provides automatic customization of phylogenetic trees based on metadata and abundance information. The Iroki web app and documentation is available at http://www.iroki.net or through the VIROME portal (http://virome.dbi.udel.edu). Iroki's source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.
-%U https://www.biorxiv.org/content/biorxiv/early/2018/08/15/106138.full.pdf
+%P 106138
+%X Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal (http://virome.dbi.udel.edu). Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.
+%U https://www.biorxiv.org/content/biorxiv/early/2019/09/28/106138.full.pdf
 

manuscript_citation/iroki_-automatic-customization-and-visualization-of-phylogenetic-trees.ris

@@ -1,12 +1,14 @@
 TY  - JOUR
 T1  - Iroki: automatic customization and visualization of phylogenetic trees
 JF  - bioRxiv
-M3  - 10.1101/106138
-AU  - Moore, Ryan M
-AU  - Harrison, Amelia O
-AU  - McAllister, Sean M
+DO  - 10.1101/106138
+SP  - 106138
+AU  - Moore, Ryan M.
+AU  - Harrison, Amelia O.
+AU  - McAllister, Sean M.
+AU  - Polson, Shawn W.
 AU  - Wommack, K. Eric
-Y1  - 2018/01/01
-UR  - http://biorxiv.org/content/early/2018/08/15/106138.abstract
-N2  - Phylogenetic trees are an important analytical tool for examining community diversity and the evolutionary history of species. In the case of microorganisms, decreasing sequencing costs have enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets present challenges to the extraction of meaningful trends from complex trees. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. To address these issues, we developed Iroki, a user-friendly web interface for tree visualization that provides automatic customization of phylogenetic trees based on metadata and abundance information. The Iroki web app and documentation is available at http://www.iroki.net or through the VIROME portal (http://virome.dbi.udel.edu). Iroki's source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.
+Y1  - 2019/01/01
+UR  - http://biorxiv.org/content/early/2019/09/28/106138.abstract
+N2  - Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal (http://virome.dbi.udel.edu). Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.
 ER  - 

manuscript_citation/iroki_-automatic-customization-and-visualization-of-phylogenetic-trees.txt

@@ -0,0 +1,15 @@
+RT Journal Article
+SR Electronic
+T1 Iroki: automatic customization and visualization of phylogenetic trees
+JF bioRxiv
+FD Cold Spring Harbor Laboratory
+SP 106138
+DO 10.1101/106138
+A1 Moore, Ryan M.
+A1 Harrison, Amelia O.
+A1 McAllister, Sean M.
+A1 Polson, Shawn W.
+A1 Wommack, K. Eric
+YR 2019
+UL http://biorxiv.org/content/early/2019/09/28/106138.abstract
+AB Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal (http://virome.dbi.udel.edu). Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.