@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: a phylogenetic tree viewer for different types of tree annotations

-Version: 1.1.15

+Version: 1.1.16

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 1.1.16

+------------------------

+ o update citation <2015-08-17, Mon>

+ 

 CHANGES IN VERSION 1.1.15

 ------------------------

  o open text angle parameter for annotation_clade/annotation_clade2 <2015-08-13, Thu>

@@ -2,12 +2,16 @@ citHeader("To cite ggtree in publications use:")

 citEntry(

     entry  = "article",

-    title  = "ggtree: an R package for versatile annotation and visualization of phylogenetic tree",

+    title  = "ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data",

     author = personList(

-        as.person("Guangchuang Yu")

-    ),

-    year    = "2015",

-    journal = "in prepare",

+        as.person("Guangchuang Yu"),

+        as.person("David Smith"),

+        as.person("Huachen Zhu"),

+        as.person("Yi Guan"),

+        as.person("Tommy Tsan-Yuk Lam")

+        ),

+    year    = "submitted",

+    journal = "Methods in Ecology and Evolution",

     volume  = "",

     issue   = "",

     number  = "",

@@ -15,7 +19,8 @@ citEntry(

     doi     = "",

     PMID    = "",

     url     = "", 

-    textVersion =

-        "Guangchuang Yu. (2015) ggtree: an R package for versatile annotation and visualization of phylogenetic tree. in prepare"

+    textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",

+        "ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data.",

+        "Methods in Ecology and Evolution submitted")

 )

@@ -42,6 +42,15 @@ library("ggtree")

 > --- Richard Dawkins

+# Citation

+If you use `r Biocpkg("ggtree")` in published research, please cite:

+

+```

+G Yu, D Smith, H Zhu, Y Guan, TTY Lam,

+ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data.

+Methods in Ecology and Evolution submitted

+```

+

 # Introduction

 This project arose from my needs to annotate nucleotide substitutions in the phylogenetic tree, and I found that there is no tree visualization software can do this easily. Existing tree viewers are designed for displaying phylogenetic tree, but not annotating it. Although some tree viewers can displaying bootstrap values in the tree, it is hard/impossible to display other information in the tree. My first solution for displaying nucleotide substituitions in the tree is to add this information in the node/tip names and use traditional tree viewer to show it. I displayed the information in the tree successfully, but I believe this indirect approach is inefficient.