CHANGES IN VERSION 1.2.2
------------------------
 o add support of ape bootstrap analysis <2015-10-26, Mon>
   see https://github.com/GuangchuangYu/ggtree/issues/20
 o add support of ancestral sequences inferred by phangorn <2015-10-26, Mon>
   see https://github.com/GuangchuangYu/ggtree/issues/21

CHANGES IN VERSION 1.1.20
------------------------
 o fixed bug in geom_tiplab when x contains NA (eg, removing by collapse function) <2015-10-01, Thu>
 o bug fixed in %add2%, if node available use node, otherwise use label <2015-09-04, Fri>
 o bug fixed of subview for considering aes mapping of x and y <2015-09-03, Thu>
 o update vignette by adding r8s example <2015-09-02, Wed>
 o defined r8s class, see http://loco.biosci.arizona.edu/r8s/  <2015-09-02, Wed>
   + add r8s sample files
   + read.r8s, parser function
   + fortify method
   + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
 o bug fixed in fortify.multiPhylo, convert df$.id to factor of levels=names(multiPhylo_object) <2015-09-02, Wed>   
 o update scale_x_ggtree to support Date as x-axis <2015-09-01, Tue>
 o add mrsd parameter for user to specify 'most recent sampling date' for time tree <2015-09-01, Tue>
   - remove 'time_scale' parameter.
 o defined 'raxml' class for RAxML bootstrapping analysis result <2015-09-01, Tue>
   + see http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html
   + read.raxml, parser function
   + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
   + fortify.raxml method
 o bug fixed in edgeNum2nodeNum for jplace parsing jplace file <2015-09-01, Tue>
 
CHANGES IN VERSION 1.1.19
------------------------
 o use fortify instead of fortify.phylo in fortify.multiPhylo, 
   so that multiPhylo can be a list of beast/codeml or other supported objects. <2015-08-31, Mon>
 o support multiPhylo object, should use + facet_wrap or + facet_grid <2015-08-31, Mon>
 o remove dependency of EBImage and phytools to speedup the installation process of ggtree <2015-08-31, Mon>
   + these two packages is not commonly used, and will be loaded automatically when needed.
 
CHANGES IN VERSION 1.1.18
------------------------
 o layout name change to 'rectangular', 'slanted', 'circular'/'fan' for phylogram and cladogram (if branch.length = 'none')
     'unroot' is not changed. <2015-08-28. Fri>
 o implement geom_point2, geom_text2, geom_segment2 to support subsetting <2015-08-28, Fri>
     see https://github.com/hadley/ggplot2/issues/1295
 o update geom_tiplab according to geom_text2 and geom_segment2 <2015-08-28, Fri>
 o add geom_tippoint, geom_nodepoint and geom_rootpoint <2015-08-28, Fri> 
 
CHANGES IN VERSION 1.1.17
------------------------
 o bug fixed in rm.singleton.newick by adding support of scientific notation in branch length <2015-08-27, Thu>
 o bug fixed in gheatmap, remove inherit aes from ggtree <2015-08-27, Thu>
 o add 'width' parameter to add_legend, now user can specify the width of legend bar <2015-08-27, Thu>
 o add 'colnames_position' parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu> 
 o theme_transparent to make background transparent <2015-08-27, Thu>
 o subview for adding ggplot object (subview) to another ggplot object (mainview) <2015-08-27, Thu>  
 
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>
 o support changing size of add_legend <2015-08-13, Thu>
 o reroot methods for phylo and beast <2015-08-07, Fri>
 
CHANGES IN VERSION 1.1.14
------------------------
 o update paml_rst to compatible with only marginal ancestral sequence or joint ancestral sequence available <2015-08-07, Fri>
 
CHANGES IN VERSION 1.1.13
------------------------
 o implement annotation_image <2015-08-01, Sat>
 o better implementation of geom_tiplab for accepting aes mapping and auto add align dotted line <2015-08-01, Sat>
 o open group_name parameter of groupOTU/groupClade to user <2015-08-01, Sat>
 
CHANGES IN VERSION 1.1.12
------------------------
 o update vignette according to the changes <2015-07-31, Fri>
 o add mapping parameter in ggtree function <2015-07-31, Fri>
 o extend groupClade to support operating on tree view <2015-07-31, Fri>
 o extend groupOTU to support operating on tree view <2015-07-31, Fri>
 o new implementation of groupClade & groupOTU <2015-07-31, Fri>
 
CHANGES IN VERSION 1.1.11
------------------------
 o annotation_clade and annotation_clade2 functions. <2015-07-30, Thu>
 o better add_legend implementation. <2015-07-30, Thu>
 o add ... in theme_tree & theme_tree2 for accepting additional parameter. <2015-07-30, Thu>
 o better geom_tree implementation. Now we can scale the tree with aes(color=numVar). <2015-07-30, Thu>
 
CHANGES IN VERSION 1.1.10
------------------------
 o solve overlapping branches for layout = "fan" || "radial",
   that are coord_polar-ized layouts.
   see https://github.com/GuangchuangYu/ggtree/issues/6,
   contributed by Vincent Bonhomme. <2015-07-22, Wed>

CHANGES IN VERSION 1.1.9
------------------------
 o update add_legend to align legend text <2015-07-06, Mon>
 o bug fixed in internal function, getChild.df, which should not include root node if selected node is root <2015-07-01, Wed>
 o rotate function for ratating a clade by 180 degree and update vignette <2015-07-01, Wed>
 o get_taxa_name function will return taxa name vector of a selected clade <2015-06-30, Tue>
 o add example of flip function in vignette <2015-06-30, Tue>
 o flip function for exchanging positions of two selected branches <2015-06-30, Tue>
 
CHANGES IN VERSION 1.1.8
------------------------
 o update get.placement <2015-06-05, Fri>
 o edgeNum2nodeNum for converting edge number to node number for EPA/pplacer output <2015-06-04, Thu>
 o mv scale_x_gheatmap to scale_x_ggtree, which also support msaplot <2015-06-02, Tue>
 o add mask function <2015-06-02, Tue>
 
CHANGES IN VERSION 1.1.7
------------------------
 o add example of msaplot in vignette <2015-05-22, Fri>
 o msaplot for adding multiple sequence alignment <2015-05-22, Fri>
 
CHANGES IN VERSION 1.1.6
------------------------
 o add vertical_only parameter to scaleClade and set to TRUE by default.
   only vertical will be scaled by default. <2015-05-22, Fri>
 o update add_colorbar & add_legend <2015-05-21, Thu>
 o add example of add_legend and gheatmap in vignette <2015-05-18, Mon> 
 o gheatmap implementation of gplot <2015-05-18, Mon>
 o add_legend for adding evolution distance legend <2015-05-18, Mon>
 
CHANGES IN VERSION 1.1.5
------------------------
 o implement scaleClade <2015-05-12, Tue>
 
CHANGES IN VERSION 1.1.4
------------------------
 o better performance of parsing beast tree  <2015-05-11, Mon>
   + support beast tree begin with 'tree tree_1 = ' and other forms.
   + support file that only contains one evidence for some of the nodes/tips
 o update add_colorbar to auto determine the position <2015-05-04, Mon>
 o add_colorbar function <2015-04-30, Thu>
 
CHANGES IN VERSION 1.1.3
------------------------
 o add space between residue substitution (e.g. K123R / E155D) <2015-04-30, Thu>
 o remove slash line in heatmap legend <2015-04-30, Thu>
 o update vignette to add example of merge_tree <2015-04-29, Wed>
 
CHANGES IN VERSION 1.1.2
------------------------
 o in addition to parsing beast time scale tree in XXX_year[\\.\\d]*, now supports XXX/year[\\.\\d]* <2015-04-29, Wed>
 o add examples folder in inst that contains sample data <2015-04-29, Wed>
 o update gplot, now rowname of heatmap will not be displayed <2015-04-28, Tue>
 o add line break if substitution longer than 50 character <2015-04-28, Tue>
 o support calculating branch for time scale tree <2015-04-28, Tue>
 o remove parsing tip sequence from mlb and mlc file <2015-04-28, Tue>
 o remove tip.fasfile in read.paml_rst for rstfile already contains tip sequence <2015-04-28, Tue>
 o scale_color accepts user specific interval and output contains 'scale' attribute that can be used for adding legend <2015-04-28, Tue>
 o extend fortify methods to support additional fields <2015-04-28, Tue>
 o extend get.fields methods to support additional fields <2015-04-28, Tue>
 o extend tree class to support additional info by merging two tree <2015-04-28, Tue>
 o implement merge_tree function to merge two tree objects into one <2015-04-28, Tue>
 
CHANGES IN VERSION 1.1.1
------------------------
 o minor bug fixed in extracting node ID of rst file <2015-04-27, Mon>
 o update parsing beast time scale tree to support _year (originally supports _year.\\d+) <2015-04-27, Mon>
 o add Tommy in author <2015-04-27, Mon>
 
CHANGES IN VERSION 0.99.28
------------------------
 o update vignette with floating table of content <2015-04-08, Wed>
 
CHANGES IN VERSION 0.99.27
------------------------
 o bug fixed, see https://github.com/GuangchuangYu/ggtree/issues/4 <2015-03-07, Tue>

CHANGES IN VERSION 0.99.26
------------------------
 o update geom_tiplab <2015-03-31, Tue>
 o update plot method of beast <2015-03-17, Tue>
 
CHANGES IN VERSION 0.99.25
------------------------
 o implement groupClade <2015-03-13, Fri>
 
CHANGES IN VERSION 0.99.24
------------------------
 o use "round" segment end, look very better <2015-03-12, Thu>
 o update vignett <2015-03-11, Wed>
 
CHANGES IN VERSION 0.99.23
------------------------
 o mv geom_hilight to hilight <2015-03-11, Wed>
 o mv geom_phylopic to phylopic <2015-03-11, Wed>
 o implement collapse and expand for collapse and expand a selected clade <2015-03-11, Wed> 
 
CHANGES IN VERSION 0.99.22
------------------------
 o remove quote in beast tip/node labels <2015-03-10, Tue>
 
CHANGES IN VERSION 0.99.21
------------------------
 o fixed downloading png file in Windows platform, should explicitly setting mode="wb". <2015-03-03, Tue>
 
CHANGES IN VERSION 0.99.19
------------------------
 o for time scale tree inferred by BEAST, now user can use time_scale=TRUE parameter in ggtree function <2015-02-12, Thu>
 
CHANGES IN VERSION 0.99.18
------------------------
 o bug fixed in reorder the labels in gplot.heatmap <2015-02-12, Thu>
 
CHANGES IN VERSION 0.99.17
------------------------
 o add angle and branch.y variable in cladogram layout <2015-02-10, Tue>
 
CHANGES IN VERSION 0.99.16
------------------------
 o correct typo in vignette <2015-02-10, Tue>

CHANGES IN VERSION 0.99.15
------------------------
 o fully support of replace operator, %<% <2015-02-09, Mon>
 
CHANGES IN VERSION 0.99.14
------------------------
 o add example in groupOTU for adding legend manually <2015-02-09, Mon>.

CHANGES IN VERSION 0.99.13
------------------------
 o two dimensional tree <2015-02-06, Fri>
 
CHANGES IN VERSION 0.99.12
------------------------
 o update vignette <2015-02-04, Wed>
 o gzoom methods that supports all tree objects <2015-02-04, Wed>
 o geom_hilight layer for highlighting clade <2015-02-04, Wed> 
 
CHANGES IN VERSION 0.99.11
------------------------
 o add scale_color to support colored lines and text based on numerical values and update vignette <2015-02-04, Wed>
 o revised groupOTU that output index can be used in geom_text and update vignette <2015-02-04, Wed>

CHANGES IN VERSION 0.99.10
------------------------
 o support y scale by category variable <2015-02-03, Tue>
 o support order nodes by yscale <2015-02-03, Tue>

CHANGES IN VERSION 0.99.9
------------------------
 o update vignette <2015-02-02, Mon>
 
CHANGES IN VERSION 0.99.8
------------------------
 o add get.phylopic function to read the online phylo pic and convert it to grob object,
   which can be use to annotate ggplot figure using annotation_custom <2015-01-30, Fri>
 
CHANGES IN VERSION 0.99.7
------------------------
 o add angle information for 'fan' & 'unrooted' layout <2015-01-29, Thu>

CHANGES IN VERSION 0.99.6
------------------------
 o read.beast now supports support values of sets such as {x, y, z} <2015-01-19, Mon>
 o now read.beast supports characters in support values <2015-01-18, Sun>
 o add example of gzoom and groupOTU in vignette <2015-01-14, Wed> 
 o implement groupOTU methods <2015-01-14, Wed>
 o export get.offspring.tip <2015-01-14, Wed>

CHANGES IN VERSION 0.99.5
------------------------
 o move ape and ggplot2 from Depends to Imports <2015-01-12, Mon>
 o get.tipseq method for paml_rst and codeml object <2015-01-08, Thu>
 o add gzoom function, similar to zoom function in ape <2015-01-07, Wed>
 o add examples in man pages of %<% and %<+% operators <2015-01-06, Tue>
 o remove <<- and update vignette <2015-01-06, Tue>
 o update vignette and use BibTex and CSL for references <2015-01-05, Mon>  
 o update cladogram layout <2015-01-05, Mon>
 o read.baseml function and update vignette with baseml example <2015-01-04, Sun>
 o plot method for hyphy and hyphy example in vignette <2015-01-04, Sun>
 o merge all vignettes to ggtree vignette <2015-01-04, Sun>

CHANGES IN VERSION 0.99.4
------------------------
 o ggtree now support branch.length = "none" to only draw tree topology <2015-01-03, Sat> 
 o get.subs method for hyphy object <2015-01-03, Sat>
 o show, get.tree and get.subs methods of hyphy <2015-01-02, Fri> 
 o export read.hyphy <2015-01-02, Fri>
 o export hyphy class <2015-01-01, Thu>
 o plot method for beast class and get.tree method for codeml class <2014-12-31, Wed>
 o show, get.fields, get.subs and plot methods for codeml class <2014-12-30, Tue>
 o plot method for paml_rst class <2014-12-30, Tue>
 o get.subs, method for paml_rst class <2014-12-30, Tue>
 o show, plot, get.tree and fority methods for codeml_mlc class <2014-12-29, Mon>
 o codeml class <2014-12-29, Mon>
 o hyphy class and read.hyphy prototype <2014-12-27, Sat>
 o update man file and add example file of beast output <2014-12-26, Fri>
 o get.tree and get.fileds methods of beast class <2014-12-26, Fri>
 o read.beast <2014-12-26, Fri>
 o beast class and show method <2014-12-26, Fri> 
 o coplot prototype<2014-12-24, Wed>
 o parse translation matrix in beast nexus <2014-12-24, Wed>
 o extract beast stats info <2014-12-23, Tue>

CHANGES IN VERSION 0.99.3
------------------------
 o gplot function that can view a tree and an associated matrix simultaneously <2014-12-22, Mon>
 o modified vignette to show based on branch position and break the evolution distance scale <2014-12-22, Mon>
 o label and annotation can be put based on branch. <2014-12-22, Mon>
 o write.jplace and fully supports of jplace by ggtree. <2014-12-21, Sun>
 o support unrooted layout in ggplot. <2014-12-21, Sun>
 o support fan, radial, dendrogram layout in geom_tree. <2014-12-21, Sun>
 
CHANGES IN VERSION 0.99.2
------------------------
 o layout of unrooted tree, implemented equal-angle algorithm that described in Chapter 34
   of 'Inferring Phylogenies' (page 578-580) <2014-12-20, Sat>
 o add layout parameter in ggtree and geom_tree, now supports phylogram and cladogram <2014-12-20, Sat>
 o %<+% function for inserting annotation data to a tree view <2014-12-20, Sat>
 o update ggtree-treeAnnotation vignette <2014-12-20, Sat>

CHANGES IN VERSION 0.99.1
------------------------
 o %<% function for updating tree view with a new tree <2014-12-19, Fri>
 o add examples in man files <2014-12-19, Fri>

CHANGES IN VERSION 0.2.3
------------------------
 o add README.md <2014-12-19, Fri>
 o update ggtree-treeViewer vignette <2014-12-19, Fri>
 o use BiocStyle in vignette <2014-12-19, Fri>
 o geom_nplace and geom_place layer <2014-12-18, Thu>
 o add theme_tree2 theme for showing evolution distance <2014-12-18, Thu>
 o rm.singleton.newick now supports internal node like:
   ((()X, ()Y)Z)AA, in which Z is a singleton. <2014-12-15, Mon>

CHANGES IN VERSION 0.2.2
------------------------
 o rm.singleton.newick <2014-12-09, Tue>
 o as.binary method <2014-12-09, Tue>

CHANGES IN VERSION 0.2.1
------------------------
 o geom_eplace <2014-12-07, Sun>

CHANGES IN VERSION 0.2.0
------------------------
 o read.jplace to read the jplace file <2014-12-05, Fri>
 o jplace class for storing information of jplace file <2014-12-05, Fri>
 o show method of jplace class <2014-12-05, Fri>
 o get.tree method to get tree from jplace class <2014-12-05, Fri>
 o extend ggplot2 to support jplace class <2014-12-05, Fri>

CHANGES IN VERSION 0.1.1
------------------------
 o add distance legend in ggtree <2014-12-05, Fri>

CHANGES IN VERSION 0.1.0
------------------------
 o support ladderize tree <2014-12-05, Fri>
 o implement geom_tree, geom_tiplab, geom_tippoint, geom_aline and theme_tree <2014-12-04, Thu>
 o extend ggplot to support phylo object and implement ggtree function <2014-12-04, Thu>
 o implement fortify function <2014-12-04, Thu>
 o add getRoot, isRoot and getParent functions <2014-12-03, Wed>
