Plotly-rectangular-phylogram-Zika.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Plotly rectangular phylogenetic tree for Zika Virus ##"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 179,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from Bio import Phylo\n",
    "import pandas as pd\n",
    "from plotly.grid_objs import Column, Grid"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 180,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<script>requirejs.config({paths: { 'plotly': ['https://cdn.plot.ly/plotly-latest.min']},});if(!window.Plotly) {{require(['plotly'],function(plotly) {window.Plotly=plotly;});}}</script>"
      ]
     },
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from plotly.offline import download_plotlyjs, init_notebook_mode,  iplot, plot\n",
    "init_notebook_mode(connected=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "tree = Phylo.read('nextstrain_zika_tree.new', \"newick\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 182,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "                                                                            Clade(branch_length=6.555195508801959e-09, name='NODE_0000473')\n",
      "                                                                                Clade(branch_length=0.000743468348689181, name='Mex03/Mexico/2016')\n",
      "                                                                                Clade(branch_length=6.555195508801959e-09, name='NODE_0000474')\n",
      "                                                                                    Clade(branch_length=0.0010225046772579624, name='Henan/001/2016')\n",
      "                                                                                    Clade(branch_length=6.555195508801959e-09, name='NODE_0000475')\n",
      "                                                                                        Clade(branch_length=0.0009295700887208889, name='Cuba/2017/Hu0046Sa')\n",
      "                                                                                        Clade(branch_length=9.287941017048669e-05, name='NODE_0000197')\n",
      "                                                                                            Clade(branch_length=6.555195508801959e-09, name='NODE_0000476')\n",
      "                                                                                                Clade(branch_length=0.00037161093492114883, name='UNK/2016/MA_WGS16_029')\n",
      "                                                                                                Clade(branch_length=0.00027869094842928504, name='NODE_0000199')\n",
      "                                                                                                    Clade(branch_length=0.0005575910351767431, name='HND/2016/HU_ME152')\n",
      "                                                                                                    Clade(branch_length=6.555195508801959e-09, name='HND/2016/HU_ME59')\n",
      "                                                                                            Clade(branch_length=9.288985285181963e-05, name='NODE_0000200')\n",
      "                                                                                                Clade(branch_length=0.00018578596644321837, name='NODE_0000201')\n",
      "                                                                                                    Clade(branch_length=0.00046461492926553336, name='NIC/5005_13A1/2016')\n",
      "                                                                                                    Clade(branch_length=0.0005576098590376532, name='FHT1175/HON/2016')\n",
      "                                                                                                Clade(branch_length=9.288650036852605e-05, name='NODE_0000202')\n",
      "                                                                                                    Clade(branch_length=0.0003716418931348649, name='HND/2016/HU_ME136')\n",
      "                                                                                                    Clade(branch_length=0.0006506183442787387, name='NIC/5847_12B1/2016')\n",
      "                                                                                                    Clade(branch_length=9.28873702265888e-05, name='NODE_0000204')\n",
      "                                                                                                        Clade(branch_length=0.0007435251975116612, name='HND/2016/HU_ME167')\n",
      "                                                                                                        Clade(branch_length=0.0008365383727206624, name='HND/2016/HU_ME50')\n",
      "                                                                                                        Clade(branch_length=0.0007435602947379739, name='HND/2016/HU_ME178')\n",
      "                                                                        Clade(branch_length=9.287932680303182e-05, name='NODE_0000181')\n",
      "                                                                            Clade(branch_length=0.00279797298937331, name='mex39/Mexico/2016')\n",
      "                                                                            Clade(branch_length=6.555195508801959e-09, name='NODE_0000477')\n",
      "                                                                                Clade(branch_length=9.288004401550396e-05, name='NODE_0000183')\n",
      "                                                                                    Clade(branch_length=0.000557518203255431, name='HND/2016/HU_ME180')\n",
      "                                                                                    Clade(branch_length=0.0011156128748953786, name='FB_GWUH_2016')\n",
      "                                                                                Clade(branch_length=6.555195508801959e-09, name='NODE_0000478')\n",
      "                                                                                    Clade(branch_length=0.0004645748844078774, name='NODE_0000186')\n",
      "                                                                                        Clade(branch_length=0.0013018480777830296, name='NIC/6406_13A1/2016')\n",
      "                                                                                        Clade(branch_length=6.555195508801959e-09, name='NODE_0000479')\n",
      "                                                                                            Clade(branch_length=6.555195508801959e-09, name='Nica2_16')\n",
      "                                                                                            Clade(branch_length=6.555195508801959e-09, name='Nica1_16')\n",
      "                                                                                    Clade(branch_length=6.555195508801959e-09, name='NODE_0000480')\n",
      "                                                                                        Clade(branch_length=0.0006504825372328068, name='HND/2016/HU_ME137')\n",
      "                                                                                        Clade(branch_length=9.287917428863618e-05, name='NODE_0000188')\n",
      "                                                                                            Clade(branch_length=0.0011156118688886805, name='NIC/1659_13A1/2016')\n",
      "                                                                                            Clade(branch_length=0.0003716026876440597, name='HND/2016/HU_SZ76')\n",
      "                                                                                            Clade(branch_length=9.287830450984899e-05, name='NODE_0000190')\n",
      "                                                                                                Clade(branch_length=0.0014879221580915373, name='NIC/7253_13A1/2016')\n",
      "                                                                                                Clade(branch_length=0.0013018994399406209, name='NIC/1304_13A1/2016')\n",
      "                                                                                                Clade(branch_length=0.0009294749190695015, name='NIC/5338_13A1/2016')\n",
      "                                                                                                Clade(branch_length=6.555195508801959e-09, name='NODE_0000481')\n",
      "                                                                                                    Clade(branch_length=0.0007434480356881693, name='HND/2016/HU_ME171')\n",
      "                                                                                                    Clade(branch_length=6.555195508801959e-09, name='NODE_0000482')\n",
      "                                                                                                        Clade(branch_length=0.000371643248902188, name='HND/2016/HU_ME172')\n",
      "                                                                                                        Clade(branch_length=0.0002786804863937741, name='NODE_0000192')\n",
      "                                                                                                            Clade(branch_length=6.555195508801959e-09, name='HND/2016/HU_ME131')\n",
      "                                                                                                            Clade(branch_length=0.0003716033067546797, name='FHT1166/HON/2016')\n"
     ]
    }
   ],
   "source": [
    "print(tree)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 183,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#dir(tree)\n",
    "#tree.get_terminals()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 184,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#tree.count_terminals()# Counts the number of terminal (leaf) nodes within this tree."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The functions `get_x_coordinates()`, `get_y_coordinates()` are mainly the functions with the samename \n",
    "from Biopython: [https://github.com/biopython/biopython/blob/master/Bio/Phylo/_utils.py](https://github.com/biopython/biopython/blob/master/Bio/Phylo/_utils.py)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 185,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def get_x_coordinates(tree):\n",
    "    \"\"\"Associates to  each clade an x-coord.\n",
    "       returns dict {clade: x-coord}\n",
    "    \"\"\"\n",
    "    xcoords = tree.depths()\n",
    "    #tree.depth() maps tree clades to depths (by branch length).\n",
    "    #returns a dict {clade: depth} where clade runs over all Clade instances of the tree, and depth is the distance from root\n",
    "    #to clade\n",
    "    \n",
    "    #  If there are no branch lengths, assign unit branch lengths\n",
    "    if not max(xcoords.values()):\n",
    "        xcoords = tree.depths(unit_branch_lengths=True)\n",
    "    return xcoords\n",
    "   \n",
    "def get_y_coordinates(tree, dist=1.3):\n",
    "    \"\"\"\n",
    "       returns  dict {clade: y-coord}\n",
    "       The y-coordinates are  (float) multiple of integers (i*dist below)\n",
    "       dist depends on the number of tree leafs\n",
    "        \"\"\"\n",
    "    maxheight = tree.count_terminals()#Counts the number of tree leafs.\n",
    "    # Rows are defined by the tips/leafs\n",
    "    ycoords = dict((leaf, maxheight - i*dist) for i, leaf in enumerate(reversed(tree.get_terminals())))\n",
    "    def calc_row(clade):\n",
    "            for subclade in clade:\n",
    "                if subclade not in ycoords:\n",
    "                    calc_row(subclade)\n",
    "            ycoords[clade] = (ycoords[clade.clades[0]] +\n",
    "                              ycoords[clade.clades[-1]]) / 2\n",
    "\n",
    "    if tree.root.clades:\n",
    "        calc_row(tree.root)\n",
    "    return ycoords\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 186,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{Clade(branch_length=0.0, name='NODE_0000385'): 0, Clade(branch_length=6.555195508771621e-09, name='NODE_0000349'): 6.555195508771621e-09, Clade(branch_length=0.005791682797542086, name='NIID123/2016'): 0.005791689352737594, Clade(branch_length=0.004384661968494351, name='NODE_0000355'): 0.00438466852368986, Clade(branch_length=0.0005576851603132952, name='ZKA_16_097'): 0.004942353684003155, Clade(branch_length=0.0006507515846834455, name='SG_108'): 0.005035420108373306, Clade(branch_length=9.291026105521637e-05, name='NODE_0000363'): 0.0044775787847450765, Clade(branch_length=6.555195508801959e-09, name='SG_037'): 0.004477585339940585, Clade(branch_length=9.291097893227018e-05, name='NODE_0000365'): 0.004570489763677347, Clade(branch_length=0.0003717753998666298, name='SG_046'): 0.0049422651635439765, Clade(branch_length=0.00018585767239837157, name='SG_027'): 0.004756347436075718, Clade(branch_length=6.555195508801959e-09, name='NODE_0000483'): 0.004384675078885369, Clade(branch_length=9.290947432497292e-05, name='NODE_0000380'): 0.004477584553210342, Clade(branch_length=0.00027877872499755627, name='SG_109'): 0.004756363278207898, Clade(branch_length=9.290947433932863e-05, name='SG_111'): 0.0045704940275496705, Clade(branch_length=6.555195508801959e-09, name='NODE_0000484'): 0.004384681634080878, Clade(branch_length=0.00018583530356231556, name='SG_063'): 0.004570516937643193, Clade(branch_length=6.555195508801959e-09, name='NODE_0000485'): 0.0043846881892763865, Clade(branch_length=9.290947432497292e-05, name='NODE_0000373'): 0.0044775976636013595, Clade(branch_length=6.555195508801959e-09, name='SG_105'): 0.004477604218796868, Clade(branch_length=9.290947433932863e-05, name='NODE_0000374'): 0.004570507137940688, Clade(branch_length=9.291132535257929e-05, name='SG_020'): 0.004663418463293267, Clade(branch_length=6.555195508801959e-09, name='SG_016'): 0.004570513693136197, Clade(branch_length=6.555195508801959e-09, name='NODE_0000486'): 0.004384694744471895, Clade(branch_length=9.291034462908989e-05, name='NODE_0000358'): 0.004477605089100985, Clade(branch_length=0.00018583704705949639, name='SG_013'): 0.004663442136160482, Clade(branch_length=6.555195508801959e-09, name='SG_061'): 0.004477611644296494, Clade(branch_length=6.555195508801959e-09, name='NODE_0000487'): 0.004384701299667404, Clade(branch_length=9.292894037943745e-05, name='NODE_0000359'): 0.004477630240046842, Clade(branch_length=9.290533770798474e-05, name='SG_008'): 0.004570535577754826, Clade(branch_length=6.555195508801959e-09, name='NODE_0000488'): 0.00447763679524235, Clade(branch_length=6.555195508801959e-09, name='SG_005'): 0.004477643350437859, Clade(branch_length=6.555195508801959e-09, name='NODE_0000489'): 0.004477643350437859, Clade(branch_length=6.555195508801959e-09, name='SG_097'): 0.004477649905633368, Clade(branch_length=6.555195508801959e-09, name='SG_014'): 0.004477649905633368, Clade(branch_length=6.555195508801959e-09, name='NODE_0000490'): 0.004384707854862913, Clade(branch_length=9.290962685398405e-05, name='SG_009'): 0.004477617481716897, Clade(branch_length=6.555195508801959e-09, name='NODE_0000386'): 0.004384714410058422, Clade(branch_length=9.291369890522799e-05, name='SG_025'): 0.00447762810896365, Clade(branch_length=6.555195508801959e-09, name='NODE_0000387'): 0.0043847209652539305, Clade(branch_length=6.555195508801959e-09, name='SG_102'): 0.004384727520449439, Clade(branch_length=6.555195508801959e-09, name='NODE_0000388'): 0.004384727520449439, Clade(branch_length=6.555195508801959e-09, name='SG_095'): 0.004384734075644948, Clade(branch_length=6.555195508801959e-09, name='NODE_0000389'): 0.004384734075644948, Clade(branch_length=6.555195508801959e-09, name='SG_033'): 0.004384740630840457, Clade(branch_length=6.555195508801959e-09, name='NODE_0000390'): 0.004384740630840457, Clade(branch_length=6.555195508801959e-09, name='SG_100'): 0.004384747186035966, Clade(branch_length=6.555195508801959e-09, name='NODE_0000391'): 0.004384747186035966, Clade(branch_length=6.555195508801959e-09, name='SG_041'): 0.0043847537412314746, Clade(branch_length=6.555195508801959e-09, name='NODE_0000392'): 0.0043847537412314746, Clade(branch_length=6.555195508801959e-09, name='SG_090'): 0.004384760296426983, Clade(branch_length=6.555195508801959e-09, name='NODE_0000393'): 0.004384760296426983, Clade(branch_length=6.555195508801959e-09, name='SG_073'): 0.004384766851622492, Clade(branch_length=6.555195508801959e-09, name='SG_039'): 0.004384766851622492, Clade(branch_length=0.0012088403113641886, name='NODE_0000348'): 0.0012088403113641886, Clade(branch_length=0.0012088490956621734, name='1_0038_PF'): 0.002417689407026362, Clade(branch_length=9.289304552495526e-05, name='NODE_0000333'): 0.001301733356889144, Clade(branch_length=0.0006506373034487578, name='1_0111_PF'): 0.0019523706603379017, Clade(branch_length=0.00046467257620650716, name='1_0030_PF'): 0.001766405933095651, Clade(branch_length=6.555195508801959e-09, name='NODE_0000394'): 0.0013017399120846527, Clade(branch_length=9.289296201114481e-05, name='NODE_0000328'): 0.0013946328740957975, Clade(branch_length=0.0004646097457009369, name='1_0035_PF'): 0.0018592426197967344, Clade(branch_length=6.555195508801959e-09, name='NODE_0000395'): 0.0013946394292913063, Clade(branch_length=0.0002787524309802113, name='H/PF/2013'): 0.0016733918602715176, Clade(branch_length=6.555195508801959e-09, name='NODE_0000396'): 0.0013946459844868151, Clade(branch_length=0.0003716602024022779, name='1_0080_PF'): 0.001766306186889093, Clade(branch_length=0.00018579890963822264, name='1_0087_PF'): 0.0015804448941250378, Clade(branch_length=0.0006505790208789167, name='NODE_0000334'): 0.0019523189329635694, Clade(branch_length=9.289454960175565e-05, name='NODE_0000335'): 0.002045213482565325, Clade(branch_length=0.002980689664419534, name='Chiba/S36/2016'): 0.005025903146984859, Clade(branch_length=0.000743601807765319, name='TS17_2016'): 0.002788815290330644, Clade(branch_length=0.0013952080105308394, name='NODE_0000336'): 0.003347526943494409, Clade(branch_length=6.555195508801959e-09, name='ZJ02'): 0.0033475334986899177, Clade(branch_length=9.290465075146226e-05, name='NODE_0000337'): 0.003440431594245871, Clade(branch_length=0.0003717146107576415, name='ZJ03'): 0.0038121462050035126, Clade(branch_length=0.0002787625279460559, name='NODE_0000338'): 0.003719194122191927, Clade(branch_length=9.290416913719339e-05, name='Zhejiang04'): 0.0038120982913291204, Clade(branch_length=9.290480330151384e-05, name='NODE_0000339'): 0.003812098925493441, Clade(branch_length=6.555195508801959e-09, name='CN/SZ02/2016'): 0.0038121054806889497, Clade(branch_length=0.0001858240637959709, name='SZ_WIV01'): 0.003997922989289412, Clade(branch_length=9.291509912518229e-05, name='NODE_0000340'): 0.003905014024618623, Clade(branch_length=9.291102706754546e-05, name='ZJ04'): 0.003997925051686169, Clade(branch_length=9.291174485968803e-05, name='ZJ01'): 0.003997925769478311, Clade(branch_length=9.291087448795934e-05, name='SZ01/2016/China'): 0.0039979248991065825, Clade(branch_length=0.0001858240637959709, name='NODE_0000344'): 0.003997922989289412, Clade(branch_length=6.555195508801959e-09, name='SMGC_1'): 0.003997929544484921, Clade(branch_length=6.555195508801959e-09, name='NODE_0000397'): 0.003997929544484921, Clade(branch_length=0.00037178660802780414, name='NODE_0000347'): 0.004369716152512725, Clade(branch_length=6.555195508801959e-09, name='_CCMU01/2016'): 0.0043697227077082335, Clade(branch_length=6.555195508801959e-09, name='SY01_2016'): 0.0043697227077082335, Clade(branch_length=6.555195508801959e-09, name='NODE_0000398'): 0.003997936099680429, Clade(branch_length=6.555195508801959e-09, name='Z16006'): 0.003997942654875938, Clade(branch_length=6.555195508801959e-09, name='ZKC2/2016'): 0.003997942654875938, Clade(branch_length=9.289232800203462e-05, name='NODE_0000323'): 0.0013946256848911785, Clade(branch_length=0.0008368969403068742, name='1_0016_PF'): 0.0022315226251980527, Clade(branch_length=0.0005575825675959499, name='1_0015_PF'): 0.0019522082524871284, Clade(branch_length=9.289154154413777e-05, name='NODE_0000325'): 0.0014875172264353163, Clade(branch_length=0.00037165635690489837, name='1_0134_PF'): 0.0018591735833402147, Clade(branch_length=9.289145800194486e-05, name='1_0199_PF'): 0.0015804086844372612, Clade(branch_length=9.289169403947162e-05, name='NODE_0000322'): 0.0014875173789306501, Clade(branch_length=0.00018579811238057906, name='PF13/251013_18'): 0.0016733154913112292, Clade(branch_length=0.00018579684234499043, name='1_0181_PF'): 0.0016733142212756406, Clade(branch_length=0.0002787250504805738, name='NODE_0000320'): 0.0016733507353717523, Clade(branch_length=0.0003716893261028857, name='1_0049_PF'): 0.002045040061474638, Clade(branch_length=0.00027872788187560107, name='1_0117_PF'): 0.0019520786172473534, Clade(branch_length=0.00027872788187560107, name='NODE_0000309'): 0.0019520786172473534, Clade(branch_length=0.0005576245900686698, name='NODE_0000310'): 0.002509703207316023, Clade(branch_length=0.0008366915232222256, name='Haiti/1/2016'): 0.0033463947305382487, Clade(branch_length=0.0002787175141836513, name='NODE_0000311'): 0.0027884207214996745, Clade(branch_length=6.555195508801959e-09, name='Haiti/1225/2014'): 0.0027884272766951833, Clade(branch_length=0.00046459957337844195, name='NODE_0000312'): 0.0032530202948781164, Clade(branch_length=6.555195508801959e-09, name='SPH2015'): 0.003253026850073625, Clade(branch_length=9.289844765418944e-05, name='NODE_0000313'): 0.003345918742532306, Clade(branch_length=6.555195508801959e-09, name='V17829'): 0.0033459252977278147, Clade(branch_length=0.00018580065237958814, name='PE243'): 0.003531719394911894, Clade(branch_length=0.000278733601777451, name='Brazil/PE243/2015'): 0.003624652344309757, 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     ]
    }
   ],
   "source": [
    "x_coords = get_x_coordinates(tree)\n",
    "y_coords = get_y_coordinates(tree)\n",
    "                             \n",
    "print(x_coords)\n",
    "print(y_coords)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 187,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def get_clade_lines(orientation='horizontal', y_curr=0, x_start=0, x_curr=0, y_bot=0, y_top=0,\n",
    "                    line_color='rgb(25,25,25)', line_width=0.5):\n",
    "    \"\"\"define a shape of type 'line', for branch\n",
    "    \"\"\"\n",
    "    branch_line=dict(type= 'line',\n",
    "                     layer='below',\n",
    "                     line=dict(color=line_color, \n",
    "                               width=line_width)\n",
    "                     )\n",
    "    if orientation=='horizontal':\n",
    "        branch_line.update(x0=x_start,\n",
    "                           y0=y_curr,\n",
    "                           x1=x_curr,\n",
    "                           y1=y_curr)\n",
    "    elif orientation=='vertical':\n",
    "        branch_line.update(x0=x_curr,\n",
    "                           y0=y_bot,\n",
    "                           x1=x_curr,\n",
    "                           y1=y_top)\n",
    "    else:\n",
    "        raise ValueError(\"Line type can be 'horizontal' or 'vertical'\")\n",
    "       \n",
    "    return branch_line    \n",
    "        \n",
    "    \n",
    "\n",
    "def draw_clade(clade, x_start,  line_shapes,line_color='rgb(15,15,15)', line_width=1):\n",
    "    \"\"\"Recursively draw the tree branches, down from the given clade\"\"\"\n",
    "    \n",
    "    x_curr = x_coords[clade]\n",
    "    y_curr = y_coords[clade]\n",
    "   \n",
    "    # Draw a horizontal line from start to here\n",
    "    branch_line=get_clade_lines(orientation='horizontal', y_curr=y_curr, x_start=x_start, x_curr=x_curr,  \n",
    "                                line_color=line_color, line_width=line_width)\n",
    "   \n",
    "    line_shapes.append(branch_line)\n",
    "   \n",
    "    if clade.clades:\n",
    "        # Draw a vertical line connecting all children\n",
    "        y_top = y_coords[clade.clades[0]]\n",
    "        y_bot = y_coords[clade.clades[-1]]\n",
    "       \n",
    "        line_shapes.append(get_clade_lines(orientation='vertical', x_curr=x_curr, y_bot=y_bot, y_top=y_top,\n",
    "                                           line_color=line_color, line_width=line_width))\n",
    "       \n",
    "        # Draw descendants\n",
    "        for child in clade:\n",
    "            draw_clade(child, x_curr, line_shapes)\n",
    "    \n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 188,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "line_shapes=[]\n",
    "draw_clade(tree.root, 0, line_shapes, line_color='rgb(25,25,25)', line_width=1)  \n",
    " "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 189,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "my_tree_clades=x_coords.keys()\n",
    "X=[]\n",
    "Y=[]\n",
    "text=[]\n",
    "\n",
    "for cl in my_tree_clades:\n",
    "    X.append(x_coords[cl])\n",
    "    Y.append(y_coords[cl])\n",
    "    text.append(cl.name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 190,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['Strain', 'Accession', 'Date', 'Region', 'Country', 'Division',\n",
       "       'Authors', 'Journal', 'Title', 'Url', 'Num Date', 'Db', 'Raw Date'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 190,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df=pd.read_csv('nextstrain_zika_metadata.csv')\n",
    "df.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 191,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "377"
      ]
     },
     "execution_count": 191,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(df)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 192,
   "metadata": {},
   "outputs": [
    {
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       " 'Ky014312',\n",
       " 'Ky785452',\n",
       " 'Ky014310',\n",
       " 'Ky014319',\n",
       " 'Mf434521',\n",
       " 'Ky765321',\n",
       " 'Ky765317',\n",
       " 'Ky785442',\n",
       " 'Ky785421',\n",
       " 'Ky785416',\n",
       " 'Ky606273',\n",
       " 'Ku501216',\n",
       " 'Ku501217',\n",
       " 'Ky325479',\n",
       " 'Ky325465',\n",
       " 'Ky606271',\n",
       " 'Mf593625',\n",
       " 'Mf159531',\n",
       " 'Ky785454',\n",
       " 'Ky014315',\n",
       " 'Ky785418',\n",
       " 'Ky765327',\n",
       " 'Ky693677',\n",
       " 'Ky785461',\n",
       " 'Mf434520',\n",
       " 'Ky014327',\n",
       " 'Ky014311',\n",
       " 'Ky014306',\n",
       " 'Ky606274',\n",
       " 'Ky785431',\n",
       " 'Ku870645',\n",
       " 'Ky765320',\n",
       " 'Kx421194',\n",
       " 'Kx421195',\n",
       " 'Ky785444',\n",
       " 'Mf434517',\n",
       " 'Ky785471',\n",
       " 'Mf434522',\n",
       " 'Mf434516',\n",
       " 'Mf434519',\n",
       " 'Ky785448',\n",
       " 'Ky785458',\n",
       " 'Ky785414',\n",
       " 'Ky693676']"
      ]
     },
     "execution_count": 192,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "set(list(df['Region']))\n",
    "list(df['Accession'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 193,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "intermediate_node_color='rgb(100,100,100)'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Node colors (assigned  in `Plotly-rectangular-phylogram-node-colors.ipynb`)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 194,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "NA_color={'Cuba': 'rgb(252, 196, 174)',#from cm.Reds color 0.2, ... 0.8\n",
    " 'Dominican Republic': 'rgb(201, 32, 32)',\n",
    " 'El Salvador': 'rgb(253, 202, 181)',\n",
    " 'Guadeloupe': 'rgb(253, 202, 181)',\n",
    " 'Guatemala': 'rgb(252, 190, 167)',\n",
    " 'Haiti': 'rgb(252, 145, 114)',\n",
    " 'Honduras': 'rgb(239, 66, 49)',\n",
    " 'Jamaica': 'rgb(252, 185, 161)',\n",
    " 'Martinique': 'rgb(252, 190, 167)',\n",
    " 'Mexico': 'rgb(247, 109, 82)',\n",
    " 'Nicaragua': 'rgb(249, 121, 92)',\n",
    " 'Panama': 'rgb(252, 185, 161)',\n",
    " 'Puerto Rico': 'rgb(252, 174, 148)',\n",
    " 'Saint Barthelemy': 'rgb(253, 202, 181)',\n",
    " 'USA': 'rgb(188, 20, 26)',\n",
    " 'USVI': 'rgb(206, 36, 34)'}\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "SAmer_color={'Brazil': 'rgb(21, 127, 59)',# from cm.Greens colors 0.2, 0.4, 0.6, 0.8\n",
    " 'Colombia': 'rgb(153, 213, 149)',\n",
    " 'Ecuador': 'rgb(208, 237, 202)',\n",
    " 'French Guiana': 'rgb(211, 238, 205)',\n",
    " 'Peru': 'rgb(208, 237, 202)',\n",
    " 'Suriname': 'rgb(206, 236, 200)',\n",
    " 'Venezuela': 'rgb(202, 234, 196)'}\n",
    "\n",
    "\n",
    "SAsia_color={'Singapore': '#0000EE', 'Vietnam': '#1E90FF'}\n",
    "pl_SAsia=[[0.0, '#1E90FF'], [0.5, '#1E90FF'], [0.5, '#0000EE'], [1.0,'#0000EE' ]]\n",
    "\n",
    "\n",
    "Oceania_color={'American Samoa': 'rgb(209,95,238)',\n",
    " 'Fiji': 'rgb(238,130, 238)',\n",
    " 'French Polynesia': 'rgb(148,0,211)',\n",
    " 'Tonga': 'rgb(238,130, 238)'}\n",
    "\n",
    "\n",
    "China_color={'China': 'rgb(255,185,15'} \n",
    "\n",
    "JapanKorea_color={'Japan': '#fcdd04'}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 195,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "country=[]\n",
    "region=[]\n",
    "color=[intermediate_node_color]*len(X)\n",
    "\n",
    "for k, strain in enumerate(df['Strain']):\n",
    "   \n",
    "    i=text.index(strain)\n",
    "    \n",
    "    text[i]=text[i]+'<br>Country: '+'{:s}'.format(df.loc[k, 'Country'])+'<br>Region: '+'{:s}'.format(df.loc[k, 'Region'])+\\\n",
    "    '<br>Collection date: '+'{:s}'.format(df.loc[k,'Date'])+\\\n",
    "           '<br>Journal: '+'{:s}'.format(df.loc[k, 'Journal'])+'<br>Authors: '+'{:s}'.format(df.loc[k, 'Authors'])\n",
    "    country.append(df.loc[k, 'Country'])\n",
    "    region.append(df.loc[k, 'Region'])\n",
    "    if df.loc[k, 'Region']=='North America':\n",
    "        color[i]=NA_color[df.loc[k, 'Country']]\n",
    "    elif df.loc[k, 'Region']=='South America':\n",
    "        color[i]=SAmer_color[df.loc[k, 'Country']] \n",
    "    elif df.loc[k, 'Region']=='Southeast Asia':\n",
    "        color[i]=SAsia_color[df.loc[k, 'Country']]\n",
    "    elif df.loc[k, 'Region']=='Oceania':\n",
    "        color[i]=Oceania_color[df.loc[k, 'Country']] \n",
    "    elif df.loc[k, 'Region']=='China':\n",
    "        color[i]= '#fecc00'\n",
    "    elif df.loc[k, 'Region']=='Japan Korea':\n",
    "        color[i]= '#dc7928'\n",
    "    else: pass"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Define the Column(s) for the grid to be uploaded to Plotly cloud:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 207,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "axis=dict(showline=False,  \n",
    "          zeroline=False,\n",
    "          showgrid=False,\n",
    "          showticklabels=False,\n",
    "          title='' #y title\n",
    "          )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 220,
   "metadata": {},
   "outputs": [],
   "source": [
    "nodes=dict(type='scatter',\n",
    "           x=X,\n",
    "           y=Y,\n",
    "           mode='markers',\n",
    "           marker=dict(color=color,\n",
    "                       size=5),\n",
    "           text=text, #vignet information of each node\n",
    "           hoverinfo='')\n",
    "\n",
    "layout=dict(title='Phylogeny of Zika Virus<br>377 genomes colored according to region and country',\n",
    "            font=dict(family='Balto',size=14),\n",
    "            width=1000,\n",
    "            height=3000,\n",
    "            autosize=False,\n",
    "            showlegend=False,\n",
    "            xaxis=dict(showline=True,  \n",
    "                       zeroline=False,\n",
    "                       showgrid=False,\n",
    "                       ticklen=4,          \n",
    "                       showticklabels=True,\n",
    "                       title='branch length'),\n",
    "            yaxis=axis, \n",
    "            hovermode='closest',\n",
    "            shapes=line_shapes,\n",
    "            plot_bgcolor='rgb(250,250,250)',\n",
    "            margin=dict(l=10)\n",
    "           )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 221,
   "metadata": {},
   "outputs": [
    {
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Dis. 22  10  1788-1792  2016 <br>Authors: Naccache Et Al\", \"NODE_0000302\", \"Bahia02<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-05-01<br>Journal: Emerging Infect. Dis. 22  10  1788-1792  2016 <br>Authors: Naccache Et Al\", \"NODE_0000303\", \"NODE_0000304\", \"Bahia07<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-07-01<br>Journal: Emerging Infect. Dis. 22  10  1788-1792  2016 <br>Authors: Naccache Et Al\", \"NODE_0000305\", \"Bahia09<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-08-01<br>Journal: Emerging Infect. Dis. 22  10  1788-1792  2016 <br>Authors: Naccache Et Al\", \"HS_2015_BA_01<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-08-01<br>Journal: Unpublished<br>Authors: Teixeira Et Al\", \"NODE_0000306\", \"Bahia03<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-05-01<br>Journal: Emerging Infect. Dis. 22  10  1788-1792  2016 <br>Authors: Naccache Et Al\", \"NODE_0000400\", \"Bahia08<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-07-15<br>Journal: Emerging Infect. Dis. 22  10  1788-1792  2016 <br>Authors: Naccache Et Al\", \"Bahia15<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-01-01<br>Journal: Emerging Infect. Dis. 22  10  1788-1792  2016 <br>Authors: Naccache Et Al\", \"NODE_0000437\", \"NODE_0000438\", \"NODE_0000286\", \"USVI/36/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-09-13<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000287\", \"Brazil/2016/ZBRX1<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-04-18<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"NODE_0000288\", \"NODE_0000439\", \"Brazil/2016/ZBRX137<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-03-03<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"Brazil/2016/ZBRX6<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-04-19<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"NODE_0000290\", \"Brazil/2016/ZBRX103<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-05-24<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"Brazil/2016/ZBRX13<br>Country: Brazil<br>Region: South America<br>Collection date: 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America<br>Collection date: 2016-04-18<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"BRA/2016/FC_DQ42D1<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-03-23<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000442\", \"BRA/2016/FC_DQ28D1<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-03-21<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000443\", \"BRA/2016/FC_DQ47D1<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-03-28<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"Brazil/2016/ZBRY8<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-01-01<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"NODE_0000228\", \"Brazil/2016/ZBRY10<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-01-01<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"NODE_0000229\", \"Brazil_ZKV2015<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-11-30<br>Journal: Lancet Infect Dis 16  6  653-660  2016 <br>Authors: Calvet Et Al\", \"NODE_0000444\", \"NODE_0000236\", \"Brazil/2015/ZBRC301<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-05-13<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"NODE_0000445\", \"Brazil/2015/ZBRD103<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-08-20<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"NODE_0000446\", \"Brazil/2015/ZBRD107<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-09-09<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"NODE_0000238\", \"Brazil/2016/ZBRX128<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-03-13<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"Brazil/2016/INMI1<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-03-06<br>Journal: Unpublished<br>Authors: Carletti Et 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411-415  2017 <br>Authors: Metsky Et Al\", \"Brazil/2015/ZBRC313<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-06-15<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"NODE_0000448\", \"Brazil/2016/ZBRX15<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-04-24<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"Brazil/2016/ZBRC319<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-07-10<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"NODE_0000244\", \"Brazil/2015/ZBRC302<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-05-13<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"NODE_0000245\", \"NODE_0000246\", \"COL/FCC00093/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-10-07<br>Journal: Unpublished<br>Authors: Leguia Et Al\", \"NODE_0000247\", \"Colombia/2016/ZC192Se<br>Country: Colombia<br>Region: South America<br>Collection date: 2016-01-07<br>Journal: Nat Protoc 12  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America<br>Collection date: 2015-12-01<br>Journal: New Microbes New Infect 11 52-53  2016 <br>Authors: Piorkowski Et Al\", \"NODE_0000253\", \"NODE_0000449\", \"NODE_0000257\", \"Colombia/2016/ZC207Se<br>Country: Colombia<br>Region: South America<br>Collection date: 2016-01-09<br>Journal: Nat Protoc 12  6  1261-1276  2017 <br>Authors: Quick Et Al\", \"Colombia/2016/ZC199Se<br>Country: Colombia<br>Region: South America<br>Collection date: 2016-01-10<br>Journal: Nat Protoc 12  6  1261-1276  2017 <br>Authors: Quick Et Al\", \"NODE_0000450\", \"NODE_0000259\", \"Colombia/2016/ZC188Se<br>Country: Colombia<br>Region: South America<br>Collection date: 2016-01-16<br>Journal: Nat Protoc 12  6  1261-1276  2017 <br>Authors: Quick Et Al\", \"Colombia/2016/ZC204Se<br>Country: Colombia<br>Region: South America<br>Collection date: 2016-01-06<br>Journal: Nat Protoc 12  6  1261-1276  2017 <br>Authors: Quick Et Al\", \"NODE_0000451\", \"PAN/BEI_259634_V4/2016<br>Country: Panama<br>Region: North America<br>Collection date: 2016-01-01<br>Journal: Submitted  05-may-2016  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Shabman Et Al\", \"NODE_0000452\", \"NODE_0000453\", \"COL/2016/SU_1856A<br>Country: Colombia<br>Region: South America<br>Collection date: 2016-04-28<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"DOM/2016/BB_0127<br>Country: Dominican Republic<br>Region: North America<br>Collection date: 2016-04-11<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000260\", \"COL/2016/SU_2293A<br>Country: Colombia<br>Region: South America<br>Collection date: 2016-06-09<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000261\", \"COL/2016/SU_2724A<br>Country: Colombia<br>Region: South America<br>Collection date: 2016-04-05<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"COL/2016/SU_1810A<br>Country: Colombia<br>Region: South America<br>Collection date: 2016-04-06<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000263\", \"NODE_0000264\", \"FLA<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  26-apr-2017  Molecular Virology And Microbiology Baylor College Of Medicine One Baylor Plaza Houston Tx 77030 Usa<br>Authors: Kneubehl Et Al\", \"NODE_0000265\", \"PAN/CDC_259249_V1_V3/2015<br>Country: Panama<br>Region: North America<br>Collection date: 2015-12-11<br>Journal: Submitted  29-apr-2016  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Shabman Et Al\", \"PAN/CDC_259364_V1_V2/2015<br>Country: Panama<br>Region: North America<br>Collection date: 2015-12-18<br>Journal: Submitted  29-apr-2016  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Shabman Et Al\", \"NODE_0000267\", \"PAN/CDC_259359_V1_V3/2015<br>Country: Panama<br>Region: North America<br>Collection date: 2015-12-18<br>Journal: Submitted  29-apr-2016  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Shabman Et Al\", \"NODE_0000454\", \"COL/PAN_00030/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2016-12-01<br>Journal: Submitted  30-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"COL/PAN_00029/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2016-12-01<br>Journal: Submitted  30-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"NODE_0000269\", \"NODE_0000270\", \"VEN/UF_1/2016<br>Country: Venezuela<br>Region: South America<br>Collection date: 2016-03-25<br>Journal: Genome Announc 5  17  E00231-17  2017 <br>Authors: Blohm Et Al\", \"COL/UF_1/2016<br>Country: Colombia<br>Region: South America<br>Collection date: 2016-02-09<br>Journal: Unpublished<br>Authors: Lednicky Et Al\", \"NODE_0000271\", \"COL/FLR_00004/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"COL/FLR_00011/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"NODE_0000278\", \"COL/FLR_00002/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"COL/FLR_00006/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"NODE_0000279\", \"COL/FLR_00005/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"COL/FLR_00008/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"NODE_0000281\", \"COL/FLR_00016/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"COL/FLR_00014/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"NODE_0000282\", \"COL/FLR_00024/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"NODE_0000283\", \"COL/FLR_00025/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"COL/FLR_00026/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"NODE_0000455\", \"COL/FLR_00020/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"NODE_0000456\", \"COL/FLR_00017/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"COL/FLR_00001/2015<br>Country: Colombia<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  28-jul-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Pickett Et Al\", \"NODE_0000097\", \"NODE_0000100\", \"NODE_0000101\", \"FVM00318/VEN/Maracay/2016<br>Country: Venezuela<br>Region: South America<br>Collection date: 2016-10-19<br>Journal: Unpublished<br>Authors: Leguia Et Al\", \"BR/AM/16800005<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-01-08<br>Journal: Unpublished<br>Authors: Souza Et Al\", \"NODE_0000102\", \"NODE_0000103\", \"Brazil/2016/ZBRX106<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-03-07<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"NODE_0000104\", \"BeH819966<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-01-01<br>Journal: Unpublished<br>Authors: Azevedo Et Al\", \"SSABR1<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-07-01<br>Journal: Infect. Genet. Evol. 41 142-145  2016 <br>Authors: Giovanetti Et Al\", \"NODE_0000106\", \"BeH818995<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-01-01<br>Journal: Unpublished<br>Authors: Azevedo Et Al\", \"BeH815744<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-01-01<br>Journal: Unpublished<br>Authors: Azevedo Et Al\", \"NODE_0000107\", \"Z1106033<br>Country: Suriname<br>Region: South America<br>Collection date: 2015-10-02<br>Journal: Lancet 387  10015  227-228  2016 <br>Authors: Enfissi Et Al\", \"NODE_0000109\", \"BRA/2016/FC_6864<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-04-12<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"BRA/2016/FC_6863<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-04-12<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000110\", \"NODE_0000111\", \"GZ01<br>Country: Venezuela<br>Region: South America<br>Collection date: 2016-02-14<br>Journal: Unpublished<br>Authors: Deng Et Al\", \"USVI/11/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-03-22<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000113\", \"R114916<br>Country: Dominican Republic<br>Region: North America<br>Collection date: 2016-06-06<br>Journal: Submitted  23-aug-2016  Diagnostic & Reference Laboratory Arbovirus Diseases Branch Centers For Disease Control & Prevention 3150 Rampart Road Fort Collins Co 80521 Usa<br>Authors: Lanciotti Et Al\", \"NODE_0000114\", \"GZ02/2016<br>Country: Venezuela<br>Region: South America<br>Collection date: 2016-02-25<br>Journal: Unpublished<br>Authors: Li Et Al\", \"NODE_0000115\", \"Z16019<br>Country: Venezuela<br>Region: South America<br>Collection date: 2016-02-26<br>Journal: Unpublished<br>Authors: Wu Et Al\", \"GDZ16021<br>Country: China<br>Region: China<br>Collection date: 2016-02-26<br>Journal: Unpublished<br>Authors: Sun Et Al\", \"NODE_0000116\", \"BeH819015<br>Country: Brazil<br>Region: South America<br>Collection date: 2015-01-01<br>Journal: Unpublished<br>Authors: Azevedo Et Al\", \"NODE_0000117\", \"SL1602<br>Country: Suriname<br>Region: South America<br>Collection date: 2016-01-22<br>Journal: Sci Rep 7  1  2368  2017 <br>Authors: Van Boheemen Et Al\", \"NODE_0000457\", \"V17271<br>Country: French Guiana<br>Region: South America<br>Collection date: 2015-12-01<br>Journal: Submitted  25-feb-2016  Laboratoire De Virologie Institut Pasteur De La Guyane 23 Avenue Pasteur Cayenne French Guiana 97300 France<br>Authors: Enfissi Et Al\", \"NODE_0000119\", \"USVI/4/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-10-14<br>Journal: ?<br>Authors: Black Et Al\", \"NL00013<br>Country: Suriname<br>Region: South America<br>Collection date: 2016-02-11<br>Journal: Submitted  18-mar-2016  Department Of Viroscience Erasmus Medical Center Dr Molewaterplein 50 Rotterdam 3015 Ge The Netherlands<br>Authors: Stalin Raj Et Al\", \"NODE_0000121\", \"USVI/40/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-11-05<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000122\", \"NODE_0000458\", \"PRI/2016/MA_WGS16_005<br>Country: Puerto Rico<br>Region: North America<br>Collection date: 2016-04-12<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000123\", \"NODE_0000127\", \"PRVABC59<br>Country: Puerto Rico<br>Region: North America<br>Collection date: 2015-12-01<br>Journal: Emerging Infect. Dis. 22  5  933-935  2016 <br>Authors: Lanciotti Et Al\", \"PuertoRico/2016/FL008U<br>Country: Puerto Rico<br>Region: North America<br>Collection date: 2016-06-21<br>Journal: Nature  2017  In Press<br>Authors: Grubaugh Et Al\", \"BRA/2016/FC_DQ192D1<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-05-10<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000459\", \"BRA/2016/FC_DQ12D1<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-03-15<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000124\", \"PuertoRico/2016/FL016U<br>Country: Puerto Rico<br>Region: North America<br>Collection date: 2016-07-03<br>Journal: Nature  2017  In Press<br>Authors: Grubaugh Et Al\", \"NODE_0000460\", \"PRI/2016/MA_WGS16_016<br>Country: Puerto Rico<br>Region: North America<br>Collection date: 2016-06-26<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"PRI/2016/MA_WGS16_004<br>Country: Puerto Rico<br>Region: North America<br>Collection date: 2016-04-13<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000130\", \"NODE_0000131\", \"USVI/23/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-07-12<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000132\", \"NODE_0000461\", \"USVI/39/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-11-09<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000133\", \"USVI/30/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-08-07<br>Journal: ?<br>Authors: Black Et Al\", \"USVI/32/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-08-11<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000135\", \"USVI/37/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-10-06<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000136\", \"USVI/12/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-11-04<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000137\", \"USVI/1/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-09-28<br>Journal: ?<br>Authors: Black Et Al\", \"USVI/2/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-09-28<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000138\", \"USIV/35/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-09-08<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000139\", \"USVI/25/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-09-27<br>Journal: ?<br>Authors: Black Et Al\", \"USVI/27/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-08-19<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000140\", \"USVI/43/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-07-19<br>Journal: ?<br>Authors: Black Et Al\", \"USVI/34/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-08-01<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000141\", \"USVI/13/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-08-13<br>Journal: ?<br>Authors: Black Et Al\", \"USVI/38/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-10-25<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000145\", \"NODE_0000146\", \"USVI/3/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-09-26<br>Journal: ?<br>Authors: Black Et Al\", \"USVI/5/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-10-17<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000147\", \"USVI/21/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-11-07<br>Journal: ?<br>Authors: Black Et Al\", \"USVI/6/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-10-19<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000462\", \"NODE_0000098\", \"Brazil/2016/ZBRX102<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-02-25<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"USVI/24/2016<br>Country: USVI<br>Region: North America<br>Collection date: 2016-09-13<br>Journal: ?<br>Authors: Black Et Al\", \"NODE_0000148\", \"NODE_0000463\", \"NODE_0000150\", \"Brazil/2016/ZBRC16<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-01-19<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"BRA/2016/FC_6418<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-03-27<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000151\", \"BRA/2016/FC_DQ5D1<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-03-14<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"RIO_BM1<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-02-12<br>Journal: Unpublished<br>Authors: Bonaldo Et Al\", \"NODE_0000464\", \"Brazil/2016/ZBRY7<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-01-01<br>Journal: Nature 546  7658  406-410  2017 <br>Authors: Faria Et Al\", \"NODE_0000465\", \"BRA/2016/FC_5905<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-03-23<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"Brazil/2016/ZBRY1<br>Country: Brazil<br>Region: South America<br>Collection date: 2016-01-15<br>Journal: Unpublished<br>Authors: Faria Et Al\", \"NODE_0000155\", \"NIC/6188_13A1/2016<br>Country: Nicaragua<br>Region: North America<br>Collection date: 2016-06-30<br>Journal: Submitted  13-mar-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Shabman Et Al\", \"NODE_0000156\", \"NODE_0000157\", \"2016\\\\HND\\\\19563<br>Country: Honduras<br>Region: North America<br>Collection date: 2016-04-16<br>Journal: ?<br>Authors: ?\", \"NODE_0000158\", \"V103451<br>Country: Honduras<br>Region: North America<br>Collection date: 2016-01-06<br>Journal: Submitted  18-may-2016  Diagnostic & Reference Laboratory Arbovirus Diseases Branch Centers For Disease Control & Prevention 3150 Rampart Road Fort Collins Co 80521 Usa<br>Authors: Lanciotti Et Al\", \"HND/R103451/2015<br>Country: Honduras<br>Region: North America<br>Collection date: 2015-01-06<br>Journal: Submitted  12-aug-2016  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Shabman Et Al\", \"NODE_0000206\", \"Mexico_Rus_10GNN_2016<br>Country: Mexico<br>Region: North America<br>Collection date: 2016-11-09<br>Journal: Unpublished<br>Authors: Karan Et Al\", \"NODE_0000214\", \"mex07/Mexico/2016<br>Country: Mexico<br>Region: North America<br>Collection date: 2016-08-05<br>Journal: Unpublished<br>Authors: Chiu Et Al\", \"NODE_0000215\", \"MEX_ENCB165<br>Country: Mexico<br>Region: North America<br>Collection date: 2015-10-15<br>Journal: Unpublished<br>Authors: Sevilla-reyes Et Al\", \"ENCB165P4<br>Country: Mexico<br>Region: North America<br>Collection date: 2015-10-15<br>Journal: Unpublished<br>Authors: Sevilla-reyes Et Al\", \"NODE_0000217\", \"USA/UT_1/2016<br>Country: Mexico<br>Region: North America<br>Collection date: 2016-01-01<br>Journal: N. Engl. J. Med. 375  19  1907-1909  2016 <br>Authors: Swaminathan Et Al\", \"R116265<br>Country: Mexico<br>Region: North America<br>Collection date: 2016-06-23<br>Journal: Submitted  23-aug-2016  Diagnostic & Reference Laboratory Arbovirus Diseases Branch Centers For Disease Control & Prevention 3150 Rampart Road Fort Collins Co 80521 Usa<br>Authors: Lanciotti Et Al\", \"NODE_0000468\", \"NODE_0000207\", \"Aedes_aegypti/MEX/MEX_I_44/2016<br>Country: Mexico<br>Region: North America<br>Collection date: 2016-01-01<br>Journal: Submitted  22-feb-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Shabman Et Al\", \"Aedes_sp/MEX_I_44/2016<br>Country: Mexico<br>Region: North America<br>Collection date: 2016-01-01<br>Journal: Unpublished<br>Authors: Balaraman Et Al\", \"NODE_0000469\", \"Mexico_Rus_12TVR_2017<br>Country: Mexico<br>Region: North America<br>Collection date: 2017-01-30<br>Journal: Unpublished<br>Authors: Karan Et Al\", \"NODE_0000211\", \"MEX_CIENI551<br>Country: Mexico<br>Region: North America<br>Collection date: 2016-03-03<br>Journal: Unpublished<br>Authors: Boukadida Et Al\", \"NODE_0000212\", \"Aedessp/MEX/MEX_2_81/2016<br>Country: Mexico<br>Region: North America<br>Collection date: 2016-01-01<br>Journal: Submitted  27-jun-2016  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Shabman Et Al\", \"NODE_0000213\", \"MEX_I_7<br>Country: Mexico<br>Region: North America<br>Collection date: 2015-11-01<br>Journal: Unpublished<br>Authors: Barrows Et Al\", \"Aedessp/MEX/MEX_I_7/2016<br>Country: Mexico<br>Region: North America<br>Collection date: 2016-01-01<br>Journal: Submitted  27-jun-2016  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Shabman Et Al\", \"NODE_0000494\", \"NODE_0000168\", \"NODE_0000169\", \"NIC/8610_13A1/2016<br>Country: Nicaragua<br>Region: North America<br>Collection date: 2016-07-07<br>Journal: Submitted  13-mar-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Shabman Et Al\", \"NIC/5256_13A1/2016<br>Country: Nicaragua<br>Region: North America<br>Collection date: 2016-08-26<br>Journal: Unpublished<br>Authors: Theze Et Al\", \"NODE_0000170\", \"NODE_0000171\", \"HN16<br>Country: Honduras<br>Region: North America<br>Collection date: 2016-05-01<br>Journal: Emerging Infect. Dis. 23  1  99-101  2017 <br>Authors: Murray Et Al\", \"NODE_0000172\", \"HND/2016/HU_ME58<br>Country: Honduras<br>Region: North America<br>Collection date: 2016-05-13<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"HND/2016/HU_ME156<br>Country: Honduras<br>Region: North America<br>Collection date: 2016-06-07<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000173\", \"HND/2016/HU_ME42<br>Country: Honduras<br>Region: North America<br>Collection date: 2016-05-09<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000174\", \"HND/2016/HU_ME38<br>Country: Honduras<br>Region: North America<br>Collection date: 2016-04-30<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000178\", \"NIC/6547_13A1/2016<br>Country: Nicaragua<br>Region: North America<br>Collection date: 2016-07-19<br>Journal: Unpublished<br>Authors: Theze Et Al\", \"NODE_0000179\", \"NIC/4886_12A1/2016<br>Country: Nicaragua<br>Region: North America<br>Collection date: 2016-07-10<br>Journal: Submitted  13-mar-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Shabman Et Al\", \"NIC/7252_12A1/2016<br>Country: Nicaragua<br>Region: North America<br>Collection date: 2016-06-29<br>Journal: Submitted  13-mar-2017  J. Craig Venter Institute 9704 Medical Center Drive Rockville Md 20850 Usa<br>Authors: Shabman Et Al\", \"NODE_0000466\", \"HND/2016/HU_ME147<br>Country: Honduras<br>Region: North America<br>Collection date: 2016-06-04<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000467\", \"USA/2016/FL019<br>Country: USA<br>Region: North America<br>Collection date: 2016-07-07<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"HND/2016/HU_ME33<br>Country: Honduras<br>Region: North America<br>Collection date: 2016-04-28<br>Journal: Nature 546  7658  411-415  2017 <br>Authors: Metsky Et Al\", \"NODE_0000470\", \"NODE_0000164\", \"mex48/Mexico/2016<br>Country: Mexico<br>Region: North America<br>Collection date: 2016-06-30<br>Journal: Unpublished<br>Authors: Chiu Et Al\", \"NODE_0000165\", \"V103344<br>Country: Guatemala<br>Region: North America<br>Collection date: 2015-12-01<br>Journal: Emerging Infect. Dis. 22  5  933-935  2016 <br>Authors: Lanciotti Et Al\", \"V8375<br>Country: Guatemala<br>Region: North America<br>Collection date: 2015-11-01<br>Journal: Emerging Infect. 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