progress_report_dco.ipynb

{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Progress Report on alignment-free issue \n",
    "## 16/1/23\n",
    "- realise the co-distance measurement."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cogent3 import load_aligned_seqs, make_seq\n",
    "import plotly.express as px\n",
    "import numpy "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_kmers(seq:str, kmer:int) -> list:\n",
    "    \"\"\"\n",
    "    Use a slide window to get k-mers in a string format sequence. \n",
    "    Return a list of k-mers.\n",
    "    \"\"\"\n",
    "    return [seq[poi:poi + kmer] for poi in range(len(seq) - kmer + 1)]\n",
    "\n",
    "def context_obj_pair(seq,context_len,obj_len) -> tuple:\n",
    "    \"\"\"\n",
    "    Pick middle sites and their flanking strings. \n",
    "    \"\"\"\n",
    "    C_gram = seq[:context_len] + seq[context_len+obj_len:]\n",
    "    O_gram = seq[context_len:context_len+obj_len]\n",
    "    return C_gram, O_gram\n",
    "\n",
    "def check_repeat_struct(S_pair, C_gram, O_gram):\n",
    "    \"\"\"\n",
    "    Update the context-object dict. which indexed by the context.\n",
    "    \"\"\"\n",
    "    if C_gram in S_pair:\n",
    "        if O_gram not in S_pair[C_gram]:\n",
    "            S_pair[C_gram].append(O_gram)\n",
    "    else:\n",
    "        S_pair[C_gram] = [O_gram]\n",
    "\n",
    "def all_pairs(genome,k,context_len,obj_len) -> dict:\n",
    "    \"\"\"\n",
    "    Generate all context-object pairs in a genome.\n",
    "    \"\"\"\n",
    "    k_mers = set(get_kmers(genome, kmer=k))\n",
    "    S_pair = {}\n",
    "    for mer in k_mers:\n",
    "        seq = make_seq(mer, moltype=\"dna\")\n",
    "        reversed_seq = str(seq.rc())\n",
    "\n",
    "        C_gram, O_gram = context_obj_pair(mer,context_len,obj_len)\n",
    "        check_repeat_struct(S_pair, C_gram, O_gram)\n",
    "\n",
    "        C_gram_rc, O_gram_rc = context_obj_pair(reversed_seq,context_len,obj_len)\n",
    "        check_repeat_struct(S_pair, C_gram_rc, O_gram_rc)\n",
    "\n",
    "    return {key:val for key, val in S_pair.items() if len(val) == 1 }\n",
    "\n",
    "def co_distance(genome1, genome2, k,context_len,obj_len) -> float:\n",
    "    \"\"\"\n",
    "    Given two genomes, compute the co-distance.\n",
    "    \"\"\"\n",
    "    genome1, genome2 = (genome1, genome2) if len(genome1) < len(genome2) else (genome2, genome1)\n",
    "    S_pair1 = all_pairs(genome1,k,context_len,obj_len)\n",
    "    S_pair2 = all_pairs(genome2,k,context_len,obj_len)\n",
    "    r=0\n",
    "    i=0\n",
    "    for C_gram in S_pair1:\n",
    "        if C_gram in S_pair2:\n",
    "            r+=1\n",
    "            if S_pair2[C_gram] != S_pair1[C_gram]:\n",
    "                i+=1\n",
    "    return 0 if r == 0 else i/r\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "#wrap in matrix\n",
    "def pair_dco(seq_coll:dict, pair_distance, k,context_len,obj_len) -> numpy.ndarray: \n",
    "    \"\"\"\n",
    "    Get a pairwise co-distance matrix. \n",
    "    \"\"\"\n",
    "    seq_names = pair_distance.names\n",
    "    num_seqs = len(seq_names)\n",
    "    dcos = numpy.zeros((num_seqs, num_seqs), dtype=float)\n",
    "\n",
    "    #calculate dco matrix\n",
    "    for x in range(num_seqs-1):\n",
    "        name1 = seq_names[x]\n",
    "        for y in range(x + 1, num_seqs):\n",
    "            name2 = seq_names[y]\n",
    "            dist = co_distance(seq_coll[name1], seq_coll[name2], k,context_len,obj_len) \n",
    "            dcos[x,y] = dist\n",
    "            dcos[y,x] = dist\n",
    "\n",
    "    return dcos\n",
    "\n",
    "\n",
    "def pair_len_diff(seq_coll:dict, pair_distance) -> numpy.ndarray: \n",
    "    \"\"\"\n",
    "    Get a length difference matrix.\n",
    "    \"\"\"\n",
    "    seq_names = pair_distance.names\n",
    "    num_seqs = len(seq_names)\n",
    "    abs_diffs = numpy.zeros((num_seqs, num_seqs), dtype=float)\n",
    "\n",
    "    #calculate length difference matrix\n",
    "    for x in range(num_seqs-1):\n",
    "        name1 = seq_names[x]\n",
    "        for y in range(x + 1, num_seqs):\n",
    "            name2 = seq_names[y]\n",
    "            abs_diff = abs(len(seq_coll[name1]) - len(seq_coll[name2]))\n",
    "            abs_diffs[x,y] = abs_diff\n",
    "            abs_diffs[y,x] = abs_diff\n",
    "\n",
    "    return abs_diffs"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load sample"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "aln = load_aligned_seqs(\"~/repos/Cogent3/tests/data/brca1.fasta\", moltype=\"dna\")\n",
    "#aln = aln.no_degenerates() ##numeric test"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
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       "\n",
       "<thead class=\"head_cell\">\n",
       "<th>names</th><th>Aardvark</th><th>AfricanEl</th><th>Anteater</th><th>AsianElep</th><th>Bandicoot</th><th>Caenolest</th><th>Cat</th><th>Chimpanzee</th><th>Cow</th><th>Dog</th><th>DogFaced</th><th>Dugong</th><th>FalseVamp</th><th>FlyingFox</th><th>FlyingLem</th><th>FlyingSqu</th><th>FreeTaile</th><th>Galago</th><th>GiantElep</th><th>GoldenMol</th><th>Gorilla</th><th>HairyArma</th><th>Hedgehog</th><th>Hippo</th><th>Horse</th><th>HowlerMon</th><th>Human</th><th>HumpbackW</th><th>Jackrabbit</th><th>LeafNose</th><th>LesserEle</th><th>LittleBro</th><th>Llama</th><th>Madagascar</th><th>Manatee</th><th>Mole</th><th>Mouse</th><th>NineBande</th><th>OldWorld</th><th>Orangutan</th><th>Pangolin</th><th>Phascogale</th><th>Pig</th><th>Rat</th><th>Rhesus</th><th>Rhino</th><th>RockHyrax</th><th>RoundEare</th><th>Sloth</th><th>SpermWhale</th><th>Tenrec</th><th>TombBat</th><th>TreeHyrax</th><th>TreeShrew</th><th>Wombat</th>\n",
       "</thead>\n",
       "<tbody>\n",
       "<tr><td class=\"index\"><span class=\"c3col_left\">Aardvark</span></td><td><span class=\"c3col_right\">0.0000</span></td><td><span class=\"c3col_right\">0.1182</span></td><td><span class=\"c3col_right\">0.1665</span></td><td><span class=\"c3col_right\">0.1203</span></td><td><span class=\"c3col_right\">0.3989</span></td><td><span class=\"c3col_right\">0.4081</span></td><td><span class=\"c3col_right\">0.1775</span></td><td><span class=\"c3col_right\">0.1701</span></td><td><span class=\"c3col_right\">0.2060</span></td><td><span class=\"c3col_right\">0.1963</span></td><td><span class=\"c3col_right\">0.1842</span></td><td><span class=\"c3col_right\">0.1175</span></td><td><span class=\"c3col_right\">0.1860</span></td><td><span class=\"c3col_right\">0.1719</span></td><td><span class=\"c3col_right\">0.1620</span></td><td><span class=\"c3col_right\">0.1871</span></td><td><span class=\"c3col_right\">0.1706</span></td><td><span class=\"c3col_right\">0.2045</span></td><td><span class=\"c3col_right\">0.2051</span></td><td><span class=\"c3col_right\">0.1543</span></td><td><span class=\"c3col_right\">0.1697</span></td><td><span class=\"c3col_right\">0.1503</span></td><td><span class=\"c3col_right\">0.2335</span></td><td><span class=\"c3col_right\">0.1844</span></td><td><span class=\"c3col_right\">0.1633</span></td><td><span class=\"c3col_right\">0.1805</span></td><td><span class=\"c3col_right\">0.1712</span></td><td><span class=\"c3col_right\">0.1774</span></td><td><span class=\"c3col_right\">0.2082</span></td><td><span class=\"c3col_right\">0.1766</span></td><td><span class=\"c3col_right\">0.1872</span></td><td><span class=\"c3col_right\">0.1848</span></td><td><span class=\"c3col_right\">0.1724</span></td><td><span class=\"c3col_right\">0.2410</span></td><td><span class=\"c3col_right\">0.1144</span></td><td><span class=\"c3col_right\">0.2045</span></td><td><span class=\"c3col_right\">0.2955</span></td><td><span class=\"c3col_right\">0.1634</span></td><td><span class=\"c3col_right\">0.2960</span></td><td><span class=\"c3col_right\">0.1708</span></td><td><span class=\"c3col_right\">0.1788</span></td><td><span class=\"c3col_right\">0.3896</span></td><td><span class=\"c3col_right\">0.1914</span></td><td><span class=\"c3col_right\">0.2902</span></td><td><span class=\"c3col_right\">0.1775</span></td><td><span class=\"c3col_right\">0.1542</span></td><td><span class=\"c3col_right\">0.1726</span></td><td><span class=\"c3col_right\">0.2596</span></td><td><span class=\"c3col_right\">0.1529</span></td><td><span class=\"c3col_right\">0.1788</span></td><td><span class=\"c3col_right\">0.2696</span></td><td><span class=\"c3col_right\">0.1808</span></td><td><span class=\"c3col_right\">0.1741</span></td><td><span class=\"c3col_right\">0.1983</span></td><td><span class=\"c3col_right\">0.3888</span></td></tr>\n",
       "<tr><td class=\"index\"><span class=\"c3col_left\">AfricanEl</span></td><td><span class=\"c3col_right\">0.1182</span></td><td><span class=\"c3col_right\">0.0000</span></td><td><span class=\"c3col_right\">0.1496</span></td><td><span class=\"c3col_right\">0.0043</span></td><td><span class=\"c3col_right\">0.3925</span></td><td><span class=\"c3col_right\">0.3973</span></td><td><span class=\"c3col_right\">0.1675</span></td><td><span class=\"c3col_right\">0.1552</span></td><td><span class=\"c3col_right\">0.1918</span></td><td><span class=\"c3col_right\">0.1841</span></td><td><span class=\"c3col_right\">0.1729</span></td><td><span class=\"c3col_right\">0.0755</span></td><td><span class=\"c3col_right\">0.1674</span></td><td><span class=\"c3col_right\">0.1624</span></td><td><span class=\"c3col_right\">0.1481</span></td><td><span class=\"c3col_right\">0.1763</span></td><td><span class=\"c3col_right\">0.1623</span></td><td><span class=\"c3col_right\">0.1937</span></td><td><span class=\"c3col_right\">0.1986</span></td><td><span class=\"c3col_right\">0.1457</span></td><td><span class=\"c3col_right\">0.1549</span></td><td><span class=\"c3col_right\">0.1316</span></td><td><span class=\"c3col_right\">0.2175</span></td><td><span class=\"c3col_right\">0.1681</span></td><td><span class=\"c3col_right\">0.1449</span></td><td><span class=\"c3col_right\">0.1646</span></td><td><span class=\"c3col_right\">0.1574</span></td><td><span class=\"c3col_right\">0.1596</span></td><td><span class=\"c3col_right\">0.1976</span></td><td><span class=\"c3col_right\">0.1648</span></td><td><span class=\"c3col_right\">0.1756</span></td><td><span class=\"c3col_right\">0.1686</span></td><td><span class=\"c3col_right\">0.1559</span></td><td><span class=\"c3col_right\">0.2388</span></td><td><span class=\"c3col_right\">0.0753</span></td><td><span class=\"c3col_right\">0.1898</span></td><td><span class=\"c3col_right\">0.2898</span></td><td><span class=\"c3col_right\">0.1486</span></td><td><span class=\"c3col_right\">0.2782</span></td><td><span class=\"c3col_right\">0.1552</span></td><td><span class=\"c3col_right\">0.1625</span></td><td><span class=\"c3col_right\">0.3798</span></td><td><span class=\"c3col_right\">0.1806</span></td><td><span class=\"c3col_right\">0.2800</span></td><td><span class=\"c3col_right\">0.1604</span></td><td><span class=\"c3col_right\">0.1406</span></td><td><span class=\"c3col_right\">0.1414</span></td><td><span class=\"c3col_right\">0.2434</span></td><td><span class=\"c3col_right\">0.1418</span></td><td><span class=\"c3col_right\">0.1619</span></td><td><span class=\"c3col_right\">0.2559</span></td><td><span class=\"c3col_right\">0.1677</span></td><td><span class=\"c3col_right\">0.1409</span></td><td><span class=\"c3col_right\">0.1848</span></td><td><span class=\"c3col_right\">0.3758</span></td></tr>\n",
       "<tr><td class=\"index\"><span class=\"c3col_left\">Anteater</span></td><td><span class=\"c3col_right\">0.1665</span></td><td><span class=\"c3col_right\">0.1496</span></td><td><span class=\"c3col_right\">0.0000</span></td><td><span class=\"c3col_right\">0.1503</span></td><td><span class=\"c3col_right\">0.3998</span></td><td><span class=\"c3col_right\">0.4051</span></td><td><span class=\"c3col_right\">0.1590</span></td><td><span class=\"c3col_right\">0.1555</span></td><td><span class=\"c3col_right\">0.1892</span></td><td><span class=\"c3col_right\">0.1782</span></td><td><span class=\"c3col_right\">0.1674</span></td><td><span class=\"c3col_right\">0.1374</span></td><td><span class=\"c3col_right\">0.1694</span></td><td><span class=\"c3col_right\">0.1583</span></td><td><span class=\"c3col_right\">0.1405</span></td><td><span class=\"c3col_right\">0.1721</span></td><td><span class=\"c3col_right\">0.1582</span></td><td><span class=\"c3col_right\">0.1930</span></td><td><span class=\"c3col_right\">0.2333</span></td><td><span class=\"c3col_right\">0.1729</span></td><td><span class=\"c3col_right\">0.1555</span></td><td><span class=\"c3col_right\">0.1019</span></td><td><span class=\"c3col_right\">0.2167</span></td><td><span class=\"c3col_right\">0.1651</span></td><td><span class=\"c3col_right\">0.1466</span></td><td><span class=\"c3col_right\">0.1658</span></td><td><span class=\"c3col_right\">0.1591</span></td><td><span class=\"c3col_right\">0.1536</span></td><td><span class=\"c3col_right\">0.1965</span></td><td><span class=\"c3col_right\">0.1596</span></td><td><span class=\"c3col_right\">0.2168</span></td><td><span class=\"c3col_right\">0.1701</span></td><td><span class=\"c3col_right\">0.1600</span></td><td><span class=\"c3col_right\">0.2592</span></td><td><span class=\"c3col_right\">0.1363</span></td><td><span class=\"c3col_right\">0.1929</span></td><td><span class=\"c3col_right\">0.2851</span></td><td><span class=\"c3col_right\">0.1134</span></td><td><span class=\"c3col_right\">0.2774</span></td><td><span class=\"c3col_right\">0.1577</span></td><td><span class=\"c3col_right\">0.1608</span></td><td><span class=\"c3col_right\">0.3894</span></td><td><span class=\"c3col_right\">0.1767</span></td><td><span class=\"c3col_right\">0.2779</span></td><td><span class=\"c3col_right\">0.1614</span></td><td><span class=\"c3col_right\">0.1388</span></td><td><span class=\"c3col_right\">0.2020</span></td><td><span class=\"c3col_right\">0.2471</span></td><td><span class=\"c3col_right\">0.0934</span></td><td><span class=\"c3col_right\">0.1550</span></td><td><span class=\"c3col_right\">0.2816</span></td><td><span class=\"c3col_right\">0.1672</span></td><td><span class=\"c3col_right\">0.2006</span></td><td><span class=\"c3col_right\">0.1851</span></td><td><span class=\"c3col_right\">0.3806</span></td></tr>\n",
       "<tr><td class=\"index\"><span class=\"c3col_left\">AsianElep</span></td><td><span class=\"c3col_right\">0.1203</span></td><td><span class=\"c3col_right\">0.0043</span></td><td><span class=\"c3col_right\">0.1503</span></td><td><span class=\"c3col_right\">0.0000</span></td><td><span class=\"c3col_right\">0.3933</span></td><td><span class=\"c3col_right\">0.3978</span></td><td><span class=\"c3col_right\">0.1679</span></td><td><span class=\"c3col_right\">0.1563</span></td><td><span class=\"c3col_right\">0.1937</span></td><td><span class=\"c3col_right\">0.1842</span></td><td><span class=\"c3col_right\">0.1748</span></td><td><span class=\"c3col_right\">0.0764</span></td><td><span class=\"c3col_right\">0.1685</span></td><td><span class=\"c3col_right\">0.1636</span></td><td><span class=\"c3col_right\">0.1488</span></td><td><span class=\"c3col_right\">0.1771</span></td><td><span class=\"c3col_right\">0.1627</span></td><td><span class=\"c3col_right\">0.1942</span></td><td><span class=\"c3col_right\">0.1986</span></td><td><span class=\"c3col_right\">0.1464</span></td><td><span class=\"c3col_right\">0.1556</span></td><td><span class=\"c3col_right\">0.1330</span></td><td><span class=\"c3col_right\">0.2195</span></td><td><span class=\"c3col_right\">0.1688</span></td><td><span class=\"c3col_right\">0.1449</span></td><td><span class=\"c3col_right\">0.1653</span></td><td><span class=\"c3col_right\">0.1585</span></td><td><span class=\"c3col_right\">0.1611</span></td><td><span class=\"c3col_right\">0.1992</span></td><td><span class=\"c3col_right\">0.1655</span></td><td><span class=\"c3col_right\">0.1749</span></td><td><span class=\"c3col_right\">0.1693</span></td><td><span class=\"c3col_right\">0.1578</span></td><td><span class=\"c3col_right\">0.2395</span></td><td><span class=\"c3col_right\">0.0762</span></td><td><span class=\"c3col_right\">0.1903</span></td><td><span class=\"c3col_right\">0.2891</span></td><td><span class=\"c3col_right\">0.1504</span></td><td><span class=\"c3col_right\">0.2801</span></td><td><span class=\"c3col_right\">0.1563</span></td><td><span class=\"c3col_right\">0.1622</span></td><td><span class=\"c3col_right\">0.3798</span></td><td><span class=\"c3col_right\">0.1818</span></td><td><span class=\"c3col_right\">0.2792</span></td><td><span class=\"c3col_right\">0.1612</span></td><td><span class=\"c3col_right\">0.1403</span></td><td><span class=\"c3col_right\">0.1418</span></td><td><span class=\"c3col_right\">0.2442</span></td><td><span class=\"c3col_right\">0.1425</span></td><td><span class=\"c3col_right\">0.1635</span></td><td><span class=\"c3col_right\">0.2558</span></td><td><span class=\"c3col_right\">0.1685</span></td><td><span class=\"c3col_right\">0.1412</span></td><td><span class=\"c3col_right\">0.1867</span></td><td><span class=\"c3col_right\">0.3758</span></td></tr>\n",
       "<tr><td class=\"index\"><span class=\"c3col_left\">Bandicoot</span></td><td><span class=\"c3col_right\">0.3989</span></td><td><span class=\"c3col_right\">0.3925</span></td><td><span class=\"c3col_right\">0.3998</span></td><td><span class=\"c3col_right\">0.3933</span></td><td><span class=\"c3col_right\">0.0000</span></td><td><span class=\"c3col_right\">0.2077</span></td><td><span class=\"c3col_right\">0.4121</span></td><td><span class=\"c3col_right\">0.4007</span></td><td><span class=\"c3col_right\">0.4234</span></td><td><span class=\"c3col_right\">0.4141</span></td><td><span class=\"c3col_right\">0.4195</span></td><td><span class=\"c3col_right\">0.3878</span></td><td><span class=\"c3col_right\">0.4229</span></td><td><span class=\"c3col_right\">0.4121</span></td><td><span class=\"c3col_right\">0.3981</span></td><td><span class=\"c3col_right\">0.4067</span></td><td><span class=\"c3col_right\">0.4082</span></td><td><span class=\"c3col_right\">0.4128</span></td><td><span class=\"c3col_right\">0.4286</span></td><td><span class=\"c3col_right\">0.4076</span></td><td><span class=\"c3col_right\">0.4011</span></td><td><span class=\"c3col_right\">0.3913</span></td><td><span class=\"c3col_right\">0.4360</span></td><td><span class=\"c3col_right\">0.4192</span></td><td><span class=\"c3col_right\">0.3996</span></td><td><span class=\"c3col_right\">0.4105</span></td><td><span class=\"c3col_right\">0.4048</span></td><td><span class=\"c3col_right\">0.4140</span></td><td><span class=\"c3col_right\">0.4195</span></td><td><span class=\"c3col_right\">0.4113</span></td><td><span class=\"c3col_right\">0.4122</span></td><td><span class=\"c3col_right\">0.4076</span></td><td><span class=\"c3col_right\">0.4089</span></td><td><span class=\"c3col_right\">0.4458</span></td><td><span class=\"c3col_right\">0.3905</span></td><td><span class=\"c3col_right\">0.4175</span></td><td><span class=\"c3col_right\">0.4541</span></td><td><span class=\"c3col_right\">0.3916</span></td><td><span class=\"c3col_right\">0.4654</span></td><td><span class=\"c3col_right\">0.4028</span></td><td><span class=\"c3col_right\">0.4114</span></td><td><span class=\"c3col_right\">0.1828</span></td><td><span class=\"c3col_right\">0.4137</span></td><td><span class=\"c3col_right\">0.4515</span></td><td><span class=\"c3col_right\">0.4093</span></td><td><span class=\"c3col_right\">0.3997</span></td><td><span class=\"c3col_right\">0.4163</span></td><td><span class=\"c3col_right\">0.4497</span></td><td><span class=\"c3col_right\">0.3904</span></td><td><span class=\"c3col_right\">0.4171</span></td><td><span class=\"c3col_right\">0.4609</span></td><td><span class=\"c3col_right\">0.4062</span></td><td><span class=\"c3col_right\">0.4165</span></td><td><span class=\"c3col_right\">0.4024</span></td><td><span class=\"c3col_right\">0.1503</span></td></tr>\n",
       "<tr class=\"ellipsis\"><td><span class=\"c3col_left\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td><td><span class=\"c3col_right\">...</span></td></tr>\n",
       "<tr><td class=\"index\"><span class=\"c3col_left\">Tenrec</span></td><td><span class=\"c3col_right\">0.2696</span></td><td><span class=\"c3col_right\">0.2559</span></td><td><span class=\"c3col_right\">0.2816</span></td><td><span class=\"c3col_right\">0.2558</span></td><td><span class=\"c3col_right\">0.4609</span></td><td><span class=\"c3col_right\">0.4598</span></td><td><span class=\"c3col_right\">0.2894</span></td><td><span class=\"c3col_right\">0.2823</span></td><td><span class=\"c3col_right\">0.3031</span></td><td><span class=\"c3col_right\">0.3037</span></td><td><span class=\"c3col_right\">0.3061</span></td><td><span class=\"c3col_right\">0.2449</span></td><td><span class=\"c3col_right\">0.3034</span></td><td><span class=\"c3col_right\">0.2965</span></td><td><span class=\"c3col_right\">0.2737</span></td><td><span class=\"c3col_right\">0.3014</span></td><td><span class=\"c3col_right\">0.2960</span></td><td><span class=\"c3col_right\">0.3216</span></td><td><span class=\"c3col_right\">0.3198</span></td><td><span class=\"c3col_right\">0.2626</span></td><td><span class=\"c3col_right\">0.2812</span></td><td><span class=\"c3col_right\">0.2730</span></td><td><span class=\"c3col_right\">0.3335</span></td><td><span class=\"c3col_right\">0.2868</span></td><td><span class=\"c3col_right\">0.2770</span></td><td><span class=\"c3col_right\">0.2903</span></td><td><span class=\"c3col_right\">0.2845</span></td><td><span class=\"c3col_right\">0.2848</span></td><td><span class=\"c3col_right\">0.3101</span></td><td><span class=\"c3col_right\">0.2952</span></td><td><span class=\"c3col_right\">0.3009</span></td><td><span class=\"c3col_right\">0.2977</span></td><td><span class=\"c3col_right\">0.2896</span></td><td><span class=\"c3col_right\">0.1332</span></td><td><span class=\"c3col_right\">0.2466</span></td><td><span class=\"c3col_right\">0.3102</span></td><td><span class=\"c3col_right\">0.3633</span></td><td><span class=\"c3col_right\">0.2867</span></td><td><span class=\"c3col_right\">0.3694</span></td><td><span class=\"c3col_right\">0.2838</span></td><td><span class=\"c3col_right\">0.2970</span></td><td><span class=\"c3col_right\">0.4537</span></td><td><span class=\"c3col_right\">0.2941</span></td><td><span class=\"c3col_right\">0.3610</span></td><td><span class=\"c3col_right\">0.2896</span></td><td><span class=\"c3col_right\">0.2746</span></td><td><span class=\"c3col_right\">0.3009</span></td><td><span class=\"c3col_right\">0.3451</span></td><td><span class=\"c3col_right\">0.2775</span></td><td><span class=\"c3col_right\">0.2845</span></td><td><span class=\"c3col_right\">0.0000</span></td><td><span class=\"c3col_right\">0.2993</span></td><td><span class=\"c3col_right\">0.3024</span></td><td><span class=\"c3col_right\">0.3042</span></td><td><span class=\"c3col_right\">0.4385</span></td></tr>\n",
       "<tr><td class=\"index\"><span class=\"c3col_left\">TombBat</span></td><td><span class=\"c3col_right\">0.1808</span></td><td><span class=\"c3col_right\">0.1677</span></td><td><span class=\"c3col_right\">0.1672</span></td><td><span class=\"c3col_right\">0.1685</span></td><td><span class=\"c3col_right\">0.4062</span></td><td><span class=\"c3col_right\">0.4232</span></td><td><span class=\"c3col_right\">0.1482</span></td><td><span class=\"c3col_right\">0.1622</span></td><td><span class=\"c3col_right\">0.1743</span></td><td><span class=\"c3col_right\">0.1659</span></td><td><span class=\"c3col_right\">0.1361</span></td><td><span class=\"c3col_right\">0.1586</span></td><td><span class=\"c3col_right\">0.1333</span></td><td><span class=\"c3col_right\">0.1245</span></td><td><span class=\"c3col_right\">0.1450</span></td><td><span class=\"c3col_right\">0.1738</span></td><td><span class=\"c3col_right\">0.0956</span></td><td><span class=\"c3col_right\">0.2009</span></td><td><span class=\"c3col_right\">0.2396</span></td><td><span class=\"c3col_right\">0.2034</span></td><td><span class=\"c3col_right\">0.1622</span></td><td><span class=\"c3col_right\">0.1571</span></td><td><span class=\"c3col_right\">0.2051</span></td><td><span class=\"c3col_right\">0.1520</span></td><td><span class=\"c3col_right\">0.1299</span></td><td><span class=\"c3col_right\">0.1677</span></td><td><span class=\"c3col_right\">0.1640</span></td><td><span class=\"c3col_right\">0.1392</span></td><td><span class=\"c3col_right\">0.1950</span></td><td><span class=\"c3col_right\">0.1272</span></td><td><span class=\"c3col_right\">0.2245</span></td><td><span class=\"c3col_right\">0.1108</span></td><td><span class=\"c3col_right\">0.1460</span></td><td><span class=\"c3col_right\">0.2783</span></td><td><span class=\"c3col_right\">0.1585</span></td><td><span class=\"c3col_right\">0.1785</span></td><td><span class=\"c3col_right\">0.2948</span></td><td><span class=\"c3col_right\">0.1658</span></td><td><span class=\"c3col_right\">0.2886</span></td><td><span class=\"c3col_right\">0.1651</span></td><td><span class=\"c3col_right\">0.1405</span></td><td><span class=\"c3col_right\">0.4005</span></td><td><span class=\"c3col_right\">0.1566</span></td><td><span class=\"c3col_right\">0.2915</span></td><td><span class=\"c3col_right\">0.1675</span></td><td><span class=\"c3col_right\">0.1200</span></td><td><span class=\"c3col_right\">0.2145</span></td><td><span class=\"c3col_right\">0.1964</span></td><td><span class=\"c3col_right\">0.1545</span></td><td><span class=\"c3col_right\">0.1404</span></td><td><span class=\"c3col_right\">0.2993</span></td><td><span class=\"c3col_right\">0.0000</span></td><td><span class=\"c3col_right\">0.2114</span></td><td><span class=\"c3col_right\">0.1898</span></td><td><span class=\"c3col_right\">0.3926</span></td></tr>\n",
       "<tr><td class=\"index\"><span class=\"c3col_left\">TreeHyrax</span></td><td><span class=\"c3col_right\">0.1741</span></td><td><span class=\"c3col_right\">0.1409</span></td><td><span class=\"c3col_right\">0.2006</span></td><td><span class=\"c3col_right\">0.1412</span></td><td><span class=\"c3col_right\">0.4165</span></td><td><span class=\"c3col_right\">0.4211</span></td><td><span class=\"c3col_right\">0.2152</span></td><td><span class=\"c3col_right\">0.2041</span></td><td><span class=\"c3col_right\">0.2378</span></td><td><span class=\"c3col_right\">0.2245</span></td><td><span class=\"c3col_right\">0.2171</span></td><td><span class=\"c3col_right\">0.1302</span></td><td><span class=\"c3col_right\">0.2172</span></td><td><span class=\"c3col_right\">0.2059</span></td><td><span class=\"c3col_right\">0.1893</span></td><td><span class=\"c3col_right\">0.2168</span></td><td><span class=\"c3col_right\">0.2074</span></td><td><span class=\"c3col_right\">0.2394</span></td><td><span class=\"c3col_right\">0.2445</span></td><td><span class=\"c3col_right\">0.1949</span></td><td><span class=\"c3col_right\">0.2044</span></td><td><span class=\"c3col_right\">0.1834</span></td><td><span class=\"c3col_right\">0.2570</span></td><td><span class=\"c3col_right\">0.2213</span></td><td><span class=\"c3col_right\">0.1985</span></td><td><span class=\"c3col_right\">0.2103</span></td><td><span class=\"c3col_right\">0.2066</span></td><td><span class=\"c3col_right\">0.2106</span></td><td><span class=\"c3col_right\">0.2351</span></td><td><span class=\"c3col_right\">0.2095</span></td><td><span class=\"c3col_right\">0.2242</span></td><td><span class=\"c3col_right\">0.2172</span></td><td><span class=\"c3col_right\">0.2114</span></td><td><span class=\"c3col_right\">0.2764</span></td><td><span class=\"c3col_right\">0.1323</span></td><td><span class=\"c3col_right\">0.2347</span></td><td><span class=\"c3col_right\">0.3137</span></td><td><span class=\"c3col_right\">0.2007</span></td><td><span class=\"c3col_right\">0.3189</span></td><td><span class=\"c3col_right\">0.2037</span></td><td><span class=\"c3col_right\">0.2134</span></td><td><span class=\"c3col_right\">0.4023</span></td><td><span class=\"c3col_right\">0.2266</span></td><td><span class=\"c3col_right\">0.3079</span></td><td><span class=\"c3col_right\">0.2112</span></td><td><span class=\"c3col_right\">0.1917</span></td><td><span class=\"c3col_right\">0.0135</span></td><td><span class=\"c3col_right\">0.2875</span></td><td><span class=\"c3col_right\">0.1919</span></td><td><span class=\"c3col_right\">0.2147</span></td><td><span class=\"c3col_right\">0.3024</span></td><td><span class=\"c3col_right\">0.2114</span></td><td><span class=\"c3col_right\">0.0000</span></td><td><span class=\"c3col_right\">0.2312</span></td><td><span class=\"c3col_right\">0.4052</span></td></tr>\n",
       "<tr><td class=\"index\"><span class=\"c3col_left\">TreeShrew</span></td><td><span class=\"c3col_right\">0.1983</span></td><td><span class=\"c3col_right\">0.1848</span></td><td><span class=\"c3col_right\">0.1851</span></td><td><span class=\"c3col_right\">0.1867</span></td><td><span class=\"c3col_right\">0.4024</span></td><td><span class=\"c3col_right\">0.4070</span></td><td><span class=\"c3col_right\">0.1816</span></td><td><span class=\"c3col_right\">0.1632</span></td><td><span class=\"c3col_right\">0.2010</span></td><td><span class=\"c3col_right\">0.2016</span></td><td><span class=\"c3col_right\">0.1942</span></td><td><span class=\"c3col_right\">0.1739</span></td><td><span class=\"c3col_right\">0.1966</span></td><td><span class=\"c3col_right\">0.1814</span></td><td><span class=\"c3col_right\">0.1573</span></td><td><span class=\"c3col_right\">0.1836</span></td><td><span class=\"c3col_right\">0.1824</span></td><td><span class=\"c3col_right\">0.1953</span></td><td><span class=\"c3col_right\">0.2513</span></td><td><span class=\"c3col_right\">0.2134</span></td><td><span class=\"c3col_right\">0.1646</span></td><td><span class=\"c3col_right\">0.1675</span></td><td><span class=\"c3col_right\">0.2351</span></td><td><span class=\"c3col_right\">0.1867</span></td><td><span class=\"c3col_right\">0.1697</span></td><td><span class=\"c3col_right\">0.1798</span></td><td><span class=\"c3col_right\">0.1680</span></td><td><span class=\"c3col_right\">0.1753</span></td><td><span class=\"c3col_right\">0.2042</span></td><td><span class=\"c3col_right\">0.1914</span></td><td><span class=\"c3col_right\">0.2328</span></td><td><span class=\"c3col_right\">0.1918</span></td><td><span class=\"c3col_right\">0.1778</span></td><td><span class=\"c3col_right\">0.2854</span></td><td><span class=\"c3col_right\">0.1759</span></td><td><span class=\"c3col_right\">0.1987</span></td><td><span class=\"c3col_right\">0.2874</span></td><td><span class=\"c3col_right\">0.1827</span></td><td><span class=\"c3col_right\">0.3104</span></td><td><span class=\"c3col_right\">0.1683</span></td><td><span class=\"c3col_right\">0.1790</span></td><td><span class=\"c3col_right\">0.3872</span></td><td><span class=\"c3col_right\">0.2004</span></td><td><span class=\"c3col_right\">0.2841</span></td><td><span class=\"c3col_right\">0.1700</span></td><td><span class=\"c3col_right\">0.1604</span></td><td><span class=\"c3col_right\">0.2325</span></td><td><span class=\"c3col_right\">0.2651</span></td><td><span class=\"c3col_right\">0.1780</span></td><td><span class=\"c3col_right\">0.1772</span></td><td><span class=\"c3col_right\">0.3042</span></td><td><span class=\"c3col_right\">0.1898</span></td><td><span class=\"c3col_right\">0.2312</span></td><td><span class=\"c3col_right\">0.0000</span></td><td><span class=\"c3col_right\">0.3834</span></td></tr>\n",
       "<tr><td class=\"index\"><span class=\"c3col_left\">Wombat</span></td><td><span class=\"c3col_right\">0.3888</span></td><td><span class=\"c3col_right\">0.3758</span></td><td><span class=\"c3col_right\">0.3806</span></td><td><span class=\"c3col_right\">0.3758</span></td><td><span class=\"c3col_right\">0.1503</span></td><td><span class=\"c3col_right\">0.1740</span></td><td><span class=\"c3col_right\">0.3914</span></td><td><span class=\"c3col_right\">0.3831</span></td><td><span class=\"c3col_right\">0.4039</span></td><td><span class=\"c3col_right\">0.3962</span></td><td><span class=\"c3col_right\">0.4018</span></td><td><span class=\"c3col_right\">0.3684</span></td><td><span class=\"c3col_right\">0.4035</span></td><td><span class=\"c3col_right\">0.3916</span></td><td><span class=\"c3col_right\">0.3786</span></td><td><span class=\"c3col_right\">0.3956</span></td><td><span class=\"c3col_right\">0.3899</span></td><td><span class=\"c3col_right\">0.3976</span></td><td><span class=\"c3col_right\">0.4157</span></td><td><span class=\"c3col_right\">0.3943</span></td><td><span class=\"c3col_right\">0.3831</span></td><td><span class=\"c3col_right\">0.3720</span></td><td><span class=\"c3col_right\">0.4192</span></td><td><span class=\"c3col_right\">0.3976</span></td><td><span class=\"c3col_right\">0.3771</span></td><td><span class=\"c3col_right\">0.3934</span></td><td><span class=\"c3col_right\">0.3882</span></td><td><span class=\"c3col_right\">0.3928</span></td><td><span class=\"c3col_right\">0.4053</span></td><td><span class=\"c3col_right\">0.3911</span></td><td><span class=\"c3col_right\">0.3950</span></td><td><span class=\"c3col_right\">0.3940</span></td><td><span class=\"c3col_right\">0.3899</span></td><td><span class=\"c3col_right\">0.4245</span></td><td><span class=\"c3col_right\">0.3715</span></td><td><span class=\"c3col_right\">0.4008</span></td><td><span class=\"c3col_right\">0.4407</span></td><td><span class=\"c3col_right\">0.3741</span></td><td><span class=\"c3col_right\">0.4498</span></td><td><span class=\"c3col_right\">0.3855</span></td><td><span class=\"c3col_right\">0.3875</span></td><td><span class=\"c3col_right\">0.1358</span></td><td><span class=\"c3col_right\">0.3938</span></td><td><span class=\"c3col_right\">0.4382</span></td><td><span class=\"c3col_right\">0.3899</span></td><td><span class=\"c3col_right\">0.3790</span></td><td><span class=\"c3col_right\">0.4037</span></td><td><span class=\"c3col_right\">0.4361</span></td><td><span class=\"c3col_right\">0.3746</span></td><td><span class=\"c3col_right\">0.3961</span></td><td><span class=\"c3col_right\">0.4385</span></td><td><span class=\"c3col_right\">0.3926</span></td><td><span class=\"c3col_right\">0.4052</span></td><td><span class=\"c3col_right\">0.3834</span></td><td><span class=\"c3col_right\">0.0000</span></td></tr>\n",
       "</tbody>\n",
       "</table>\n",
       "\n",
       "</div>"
      ],
      "text/plain": [
       "=======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================\n",
       "names         Aardvark    AfricanEl    Anteater    AsianElep    Bandicoot    Caenolest       Cat    Chimpanzee       Cow       Dog    DogFaced    Dugong    FalseVamp    FlyingFox    FlyingLem    FlyingSqu    FreeTaile    Galago    GiantElep    GoldenMol    Gorilla    HairyArma    Hedgehog     Hippo     Horse    HowlerMon     Human    HumpbackW    Jackrabbit    LeafNose    LesserEle    LittleBro     Llama    Madagascar    Manatee      Mole     Mouse    NineBande    OldWorld    Orangutan    Pangolin    Phascogale       Pig       Rat    Rhesus     Rhino    RockHyrax    RoundEare     Sloth    SpermWhale    Tenrec    TombBat    TreeHyrax    TreeShrew    Wombat\n",
       "---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
       "Aardvark        0.0000       0.1182      0.1665       0.1203       0.3989       0.4081    0.1775        0.1701    0.2060    0.1963      0.1842    0.1175       0.1860       0.1719       0.1620       0.1871       0.1706    0.2045       0.2051       0.1543     0.1697       0.1503      0.2335    0.1844    0.1633       0.1805    0.1712       0.1774        0.2082      0.1766       0.1872       0.1848    0.1724        0.2410     0.1144    0.2045    0.2955       0.1634      0.2960       0.1708      0.1788        0.3896    0.1914    0.2902    0.1775    0.1542       0.1726       0.2596    0.1529        0.1788    0.2696     0.1808       0.1741       0.1983    0.3888\n",
       "AfricanEl       0.1182       0.0000      0.1496       0.0043       0.3925       0.3973    0.1675        0.1552    0.1918    0.1841      0.1729    0.0755       0.1674       0.1624       0.1481       0.1763       0.1623    0.1937       0.1986       0.1457     0.1549       0.1316      0.2175    0.1681    0.1449       0.1646    0.1574       0.1596        0.1976      0.1648       0.1756       0.1686    0.1559        0.2388     0.0753    0.1898    0.2898       0.1486      0.2782       0.1552      0.1625        0.3798    0.1806    0.2800    0.1604    0.1406       0.1414       0.2434    0.1418        0.1619    0.2559     0.1677       0.1409       0.1848    0.3758\n",
       "Anteater        0.1665       0.1496      0.0000       0.1503       0.3998       0.4051    0.1590        0.1555    0.1892    0.1782      0.1674    0.1374       0.1694       0.1583       0.1405       0.1721       0.1582    0.1930       0.2333       0.1729     0.1555       0.1019      0.2167    0.1651    0.1466       0.1658    0.1591       0.1536        0.1965      0.1596       0.2168       0.1701    0.1600        0.2592     0.1363    0.1929    0.2851       0.1134      0.2774       0.1577      0.1608        0.3894    0.1767    0.2779    0.1614    0.1388       0.2020       0.2471    0.0934        0.1550    0.2816     0.1672       0.2006       0.1851    0.3806\n",
       "AsianElep       0.1203       0.0043      0.1503       0.0000       0.3933       0.3978    0.1679        0.1563    0.1937    0.1842      0.1748    0.0764       0.1685       0.1636       0.1488       0.1771       0.1627    0.1942       0.1986       0.1464     0.1556       0.1330      0.2195    0.1688    0.1449       0.1653    0.1585       0.1611        0.1992      0.1655       0.1749       0.1693    0.1578        0.2395     0.0762    0.1903    0.2891       0.1504      0.2801       0.1563      0.1622        0.3798    0.1818    0.2792    0.1612    0.1403       0.1418       0.2442    0.1425        0.1635    0.2558     0.1685       0.1412       0.1867    0.3758\n",
       "Bandicoot       0.3989       0.3925      0.3998       0.3933       0.0000       0.2077    0.4121        0.4007    0.4234    0.4141      0.4195    0.3878       0.4229       0.4121       0.3981       0.4067       0.4082    0.4128       0.4286       0.4076     0.4011       0.3913      0.4360    0.4192    0.3996       0.4105    0.4048       0.4140        0.4195      0.4113       0.4122       0.4076    0.4089        0.4458     0.3905    0.4175    0.4541       0.3916      0.4654       0.4028      0.4114        0.1828    0.4137    0.4515    0.4093    0.3997       0.4163       0.4497    0.3904        0.4171    0.4609     0.4062       0.4165       0.4024    0.1503\n",
       "Caenolest       0.4081       0.3973      0.4051       0.3978       0.2077       0.0000    0.4163        0.4068    0.4319    0.4228      0.4202    0.3915       0.4272       0.4125       0.4044       0.4177       0.4164    0.4230       0.4444       0.4138     0.4068       0.3965      0.4345    0.4222    0.4052       0.4133    0.4111       0.4196        0.4315      0.4164       0.4241       0.4174    0.4160        0.4407     0.3931    0.4223    0.4560       0.3963      0.4796       0.4076      0.4178        0.2004    0.4232    0.4502    0.4120    0.4049       0.4196       0.4592    0.3991        0.4234    0.4598     0.4232       0.4211       0.4070    0.1740\n",
       "Cat             0.1775       0.1675      0.1590       0.1679       0.4121       0.4163    0.0000        0.1595    0.1746    0.1229      0.1566    0.1565       0.1490       0.1453       0.1473       0.1770       0.1409    0.1982       0.2449       0.1984     0.1595       0.1520      0.2021    0.1495    0.1304       0.1726    0.1623       0.1351        0.1946      0.1420       0.2217       0.1555    0.1400        0.2709     0.1563    0.1793    0.2901       0.1669      0.2817       0.1605      0.1354        0.3951    0.1620    0.2797    0.1667    0.1216       0.2167       0.2400    0.1582        0.1391    0.2894     0.1482       0.2152       0.1816    0.3914\n",
       "Chimpanzee      0.1701       0.1552      0.1555       0.1563       0.4007       0.4068    0.1595        0.0000    0.1797    0.1741      0.1680    0.1468       0.1594       0.1532       0.1235       0.1523       0.1505    0.1663       0.2419       0.1878     0.0053       0.1430      0.2145    0.1587    0.1396       0.0665    0.0092       0.1501        0.1848      0.1563       0.2131       0.1581    0.1502        0.2599     0.1464    0.1750    0.2556       0.1550      0.2678       0.0137      0.1531        0.3881    0.1688    0.2532    0.0381    0.1320       0.2055       0.2419    0.1499        0.1484    0.2823     0.1622       0.2041       0.1632    0.3831\n",
       "Cow             0.2060       0.1918      0.1892       0.1937       0.4234       0.4319    0.1746        0.1797    0.0000    0.1996      0.1801    0.1849       0.1758       0.1680       0.1735       0.1961       0.1629    0.2224       0.2547       0.2221     0.1797       0.1775      0.2309    0.1245    0.1512       0.1862    0.1805       0.1084        0.2206      0.1629       0.2448       0.1733    0.1388        0.2857     0.1823    0.1955    0.2868       0.1878      0.2967       0.1801      0.1651        0.4114    0.1499    0.2877    0.1896    0.1480       0.2375       0.2555    0.1784        0.1124    0.3031     0.1743       0.2378       0.2010    0.4039\n",
       "Dog             0.1963       0.1841      0.1782       0.1842       0.4141       0.4228    0.1229        0.1741    0.1996    0.0000      0.1821    0.1739       0.1692       0.1696       0.1602       0.1909       0.1602    0.2180       0.2549       0.2165     0.1730       0.1676      0.2309    0.1734    0.1451       0.1864    0.1765       0.1555        0.2058      0.1624       0.2440       0.1744    0.1614        0.2829     0.1733    0.1917    0.2989       0.1800      0.2935       0.1737      0.1599        0.4025    0.1804    0.2878    0.1813    0.1360       0.2257       0.2560    0.1736        0.1636    0.3037     0.1659       0.2245       0.2016    0.3962\n",
       "DogFaced        0.1842       0.1729      0.1674       0.1748       0.4195       0.4202    0.1566        0.1680    0.1801    0.1821      0.0000    0.1638       0.1408       0.0517       0.1547       0.1839       0.1278    0.2041       0.2501       0.2075     0.1672       0.1599      0.2213    0.1574    0.1406       0.1766    0.1698       0.1455        0.2011      0.1361       0.2365       0.1374    0.1556        0.2758     0.1632    0.1831    0.2991       0.1718      0.2937       0.1695      0.1498        0.4088    0.1687    0.2899    0.1749    0.1279       0.2190       0.2203    0.1604        0.1474    0.3061     0.1361       0.2171       0.1942    0.4018\n",
       "Dugong          0.1175       0.0755      0.1374       0.0764       0.3878       0.3915    0.1565        0.1468    0.1849    0.1739      0.1638    0.0000       0.1562       0.1536       0.1340       0.1615       0.1537    0.1872       0.1878       0.1269     0.1464       0.1201      0.2057    0.1604    0.1369       0.1580    0.1497       0.1475        0.1846      0.1543       0.1631       0.1631    0.1504        0.2216     0.0152    0.1794    0.2686       0.1374      0.2684       0.1468      0.1508        0.3722    0.1656    0.2644    0.1513    0.1298       0.1310       0.2360    0.1299        0.1492    0.2449     0.1586       0.1302       0.1739    0.3684\n",
       "FalseVamp       0.1860       0.1674      0.1694       0.1685       0.4229       0.4272    0.1490        0.1594    0.1758    0.1692      0.1408    0.1562       0.0000       0.1265       0.1540       0.1853       0.1229    0.2113       0.2489       0.2076     0.1587       0.1607      0.2085    0.1514    0.1288       0.1719    0.1617       0.1367        0.1943      0.1156       0.2324       0.1301    0.1447        0.2761     0.1534    0.1794    0.2929       0.1681      0.2858       0.1598      0.1411        0.4121    0.1613    0.2833    0.1664    0.1210       0.2177       0.2234    0.1664        0.1398    0.3034     0.1333       0.2172       0.1966    0.4035\n",
       "FlyingFox       0.1719       0.1624      0.1583       0.1636       0.4121       0.4125    0.1453        0.1532    0.1680    0.1696      0.0517    0.1536       0.1265       0.0000       0.1394       0.1690       0.1125    0.1936       0.2407       0.1975     0.1532       0.1442      0.2126    0.1476    0.1252       0.1599    0.1551       0.1320        0.1880      0.1197       0.2237       0.1208    0.1409        0.2706     0.1528    0.1681    0.2884       0.1571      0.2843       0.1551      0.1377        0.4010    0.1540    0.2805    0.1584    0.1134       0.2054       0.2112    0.1486        0.1351    0.2965     0.1245       0.2059       0.1814    0.3916\n",
       "FlyingLem       0.1620       0.1481      0.1405       0.1488       0.3981       0.4044    0.1473        0.1235    0.1735    0.1602      0.1547    0.1340       0.1540       0.1394       0.0000       0.1430       0.1436    0.1688       0.2274       0.1733     0.1231       0.1284      0.2045    0.1463    0.1254       0.1322    0.1266       0.1365        0.1654      0.1455       0.2122       0.1542    0.1421        0.2587     0.1344    0.1718    0.2597       0.1381      0.2594       0.1259      0.1377        0.3819    0.1538    0.2549    0.1275    0.1164       0.1914       0.2362    0.1318        0.1374    0.2737     0.1450       0.1893       0.1573    0.3786\n",
       "FlyingSqu       0.1871       0.1763      0.1721       0.1771       0.4067       0.4177    0.1770        0.1523    0.1961    0.1909      0.1839    0.1615       0.1853       0.1690       0.1430       0.0000       0.1702    0.1935       0.2528       0.2019     0.1520       0.1608      0.2303    0.1802    0.1628       0.1647    0.1562       0.1696        0.1971      0.1736       0.2291       0.1816    0.1734        0.2795     0.1641    0.1976    0.2616       0.1753      0.2627       0.1552      0.1671        0.4014    0.1885    0.2563    0.1582    0.1544       0.2165       0.2530    0.1686        0.1740    0.3014     0.1738       0.2168       0.1836    0.3956\n",
       "FreeTaile       0.1706       0.1623      0.1582       0.1627       0.4082       0.4164    0.1409        0.1505    0.1629    0.1602      0.1278    0.1537       0.1229       0.1125       0.1436       0.1702       0.0000    0.1923       0.2351       0.1958     0.1497       0.1505      0.2020    0.1423    0.1159       0.1603    0.1512       0.1293        0.1919      0.1136       0.2228       0.0856    0.1348        0.2757     0.1543    0.1693    0.2762       0.1617      0.2769       0.1523      0.1365        0.4001    0.1517    0.2719    0.1600    0.1119       0.2085       0.1975    0.1483        0.1315    0.2960     0.0956       0.2074       0.1824    0.3899\n",
       "Galago          0.2045       0.1937      0.1930       0.1942       0.4128       0.4230    0.1982        0.1663    0.2224    0.2180      0.2041    0.1872       0.2113       0.1936       0.1688       0.1935       0.1923    0.0000       0.2712       0.2219     0.1663       0.1854      0.2454    0.2000    0.1852       0.1831    0.1695       0.1927        0.2197      0.1963       0.2466       0.2027    0.1903        0.2961     0.1879    0.2190    0.3021       0.1996      0.3043       0.1681      0.1967        0.4048    0.2154    0.2928    0.1697    0.1750       0.2395       0.2840    0.1909        0.1917    0.3216     0.2009       0.2394       0.1953    0.3976\n",
       "GiantElep       0.2051       0.1986      0.2333       0.1986       0.4286       0.4444    0.2449        0.2419    0.2547    0.2549      0.2501    0.1878       0.2489       0.2407       0.2274       0.2528       0.2351    0.2712       0.0000       0.2128     0.2408       0.2181      0.2873    0.2328    0.2278       0.2514    0.2440       0.2303        0.2704      0.2406       0.2018       0.2445    0.2334        0.2991     0.1881    0.2605    0.3433       0.2267      0.3485       0.2444      0.2434        0.4164    0.2513    0.3368    0.2490    0.2170       0.2435       0.3184    0.2206        0.2308    0.3198     0.2396       0.2445       0.2513    0.4157\n",
       "GoldenMol       0.1543       0.1457      0.1729       0.1464       0.4076       0.4138    0.1984        0.1878    0.2221    0.2165      0.2075    0.1269       0.2076       0.1975       0.1733       0.2019       0.1958    0.2219       0.2128       0.0000     0.1864       0.1638      0.2471    0.2050    0.1827       0.1955    0.1904       0.1944        0.2312      0.1993       0.2008       0.2039    0.1908        0.2420     0.1262    0.2165    0.3069       0.1771      0.3046       0.1896      0.1910        0.3983    0.2080    0.2955    0.1946    0.1754       0.1945       0.2832    0.1712        0.1933    0.2626     0.2034       0.1949       0.2134    0.3943\n",
       "Gorilla         0.1697       0.1549      0.1555       0.1556       0.4011       0.4068    0.1595        0.0053    0.1797    0.1730      0.1672    0.1464       0.1587       0.1532       0.1231       0.1520       0.1497    0.1663       0.2408       0.1864     0.0000       0.1434      0.2141    0.1594    0.1392       0.0661    0.0088       0.1501        0.1852      0.1567       0.2153       0.1574    0.1495        0.2588     0.1460    0.1757    0.2563       0.1553      0.2667       0.0134      0.1534        0.3894    0.1681    0.2532    0.0378    0.1316       0.2059       0.2408    0.1506        0.1484    0.2812     0.1622       0.2044       0.1646    0.3831\n",
       "HairyArma       0.1503       0.1316      0.1019       0.1330       0.3913       0.3965    0.1520        0.1430    0.1775    0.1676      0.1599    0.1201       0.1607       0.1442       0.1284       0.1608       0.1505    0.1854       0.2181       0.1638     0.1434       0.0000      0.2102    0.1586    0.1341       0.1523    0.1448       0.1440        0.1767      0.1553       0.2039       0.1593    0.1532        0.2517     0.1208    0.1826    0.2740       0.0614      0.2667       0.1444      0.1491        0.3799    0.1653    0.2639    0.1482    0.1281       0.1844       0.2461    0.0853        0.1463    0.2730     0.1571       0.1834       0.1675    0.3720\n",
       "Hedgehog        0.2335       0.2175      0.2167       0.2195       0.4360       0.4345    0.2021        0.2145    0.2309    0.2309      0.2213    0.2057       0.2085       0.2126       0.2045       0.2303       0.2020    0.2454       0.2873       0.2471     0.2141       0.2102      0.0000    0.2078    0.1948       0.2172    0.2171       0.1984        0.2433      0.2116       0.2756       0.2133    0.1952        0.3169     0.2037    0.2113    0.3399       0.2230      0.3357       0.2160      0.2032        0.4186    0.2199    0.3307    0.2151    0.1829       0.2575       0.2852    0.2148        0.1985    0.3335     0.2051       0.2570       0.2351    0.4192\n",
       "Hippo           0.1844       0.1681      0.1651       0.1688       0.4192       0.4222    0.1495        0.1587    0.1245    0.1734      0.1574    0.1604       0.1514       0.1476       0.1463       0.1802       0.1423    0.2000       0.2328       0.2050     0.1594       0.1586      0.2078    0.0000    0.1257       0.1706    0.1598       0.0793        0.2005      0.1395       0.2207       0.1470    0.1141        0.2696     0.1580    0.1782    0.2718       0.1668      0.2786       0.1598      0.1440        0.4037    0.1224    0.2709    0.1682    0.1197       0.2210       0.2341    0.1608        0.0817    0.2868     0.1520       0.2213       0.1867    0.3976\n",
       "Horse           0.1633       0.1449      0.1466       0.1449       0.3996       0.4052    0.1304        0.1396    0.1512    0.1451      0.1406    0.1369       0.1288       0.1252       0.1254       0.1628       0.1159    0.1852       0.2278       0.1827     0.1392       0.1341      0.1948    0.1257    0.0000       0.1530    0.1424       0.1143        0.1762      0.1206       0.2128       0.1298    0.1197        0.2605     0.1351    0.1553    0.2674       0.1482      0.2660       0.1399      0.1195        0.3820    0.1411    0.2606    0.1479    0.0729       0.2007       0.2124    0.1418        0.1183    0.2770     0.1299       0.1985       0.1697    0.3771\n",
       "HowlerMon       0.1805       0.1646      0.1658       0.1653       0.4105       0.4133    0.1726        0.0665    0.1862    0.1864      0.1766    0.1580       0.1719       0.1599       0.1322       0.1647       0.1603    0.1831       0.2514       0.1955     0.0661       0.1523      0.2172    0.1706    0.1530       0.0000    0.0696       0.1580        0.1939      0.1652       0.2263       0.1658    0.1583        0.2613     0.1571    0.1864    0.2666       0.1629      0.2803       0.0679      0.1627        0.3990    0.1812    0.2631    0.0690    0.1454       0.2126       0.2459    0.1609        0.1587    0.2903     0.1677       0.2103       0.1798    0.3934\n",
       "Human           0.1712       0.1574      0.1591       0.1585       0.4048       0.4111    0.1623        0.0092    0.1805    0.1765      0.1698    0.1497       0.1617       0.1551       0.1266       0.1562       0.1512    0.1695       0.2440       0.1904     0.0088       0.1448      0.2171    0.1598    0.1424       0.0696    0.0000       0.1498        0.1882      0.1588       0.2175       0.1581    0.1498        0.2603     0.1492    0.1778    0.2582       0.1575      0.2686       0.0173      0.1538        0.3903    0.1699    0.2550    0.0410    0.1338       0.2085       0.2434    0.1524        0.1477    0.2845     0.1640       0.2066       0.1680    0.3882\n",
       "HumpbackW       0.1774       0.1596      0.1536       0.1611       0.4140       0.4196    0.1351        0.1501    0.1084    0.1555      0.1455    0.1475       0.1367       0.1320       0.1365       0.1696       0.1293    0.1927       0.2303       0.1944     0.1501       0.1440      0.1984    0.0793    0.1143       0.1580    0.1498       0.0000        0.1867      0.1289       0.2185       0.1427    0.0979        0.2635     0.1481    0.1642    0.2783       0.1539      0.2776       0.1498      0.1267        0.3966    0.1065    0.2752    0.1564    0.1084       0.2118       0.2301    0.1452        0.0254    0.2848     0.1392       0.2106       0.1753    0.3928\n",
       "Jackrabbit      0.2082       0.1976      0.1965       0.1992       0.4195       0.4315    0.1946        0.1848    0.2206    0.2058      0.2011    0.1846       0.1943       0.1880       0.1654       0.1971       0.1919    0.2197       0.2704       0.2312     0.1852       0.1767      0.2433    0.2005    0.1762       0.1939    0.1882       0.1867        0.0000      0.1905       0.2538       0.2011    0.1969        0.2911     0.1865    0.2181    0.2955       0.1921      0.2935       0.1841      0.1933        0.4050    0.2082    0.2852    0.1871    0.1745       0.2355       0.2652    0.1879        0.1917    0.3101     0.1950       0.2351       0.2042    0.4053\n",
       "LeafNose        0.1766       0.1648      0.1596       0.1655       0.4113       0.4164    0.1420        0.1563    0.1629    0.1624      0.1361    0.1543       0.1156       0.1197       0.1455       0.1736       0.1136    0.1963       0.2406       0.1993     0.1567       0.1553      0.2116    0.1395    0.1206       0.1652    0.1588       0.1289        0.1905      0.0000       0.2226       0.1253    0.1371        0.2740     0.1527    0.1759    0.2793       0.1641      0.2760       0.1563      0.1397        0.4028    0.1528    0.2747    0.1636    0.1155       0.2114       0.2121    0.1557        0.1326    0.2952     0.1272       0.2095       0.1914    0.3911\n",
       "LesserEle       0.1872       0.1756      0.2168       0.1749       0.4122       0.4241    0.2217        0.2131    0.2448    0.2440      0.2365    0.1631       0.2324       0.2237       0.2122       0.2291       0.2228    0.2466       0.2018       0.2008     0.2153       0.2039      0.2756    0.2207    0.2128       0.2263    0.2175       0.2185        0.2538      0.2226       0.0000       0.2293    0.2180        0.2826     0.1632    0.2461    0.3236       0.2151      0.3394       0.2157      0.2226        0.4025    0.2305    0.3180    0.2238    0.2021       0.2224       0.3012    0.2073        0.2179    0.3009     0.2245       0.2242       0.2328    0.3950\n",
       "LittleBro       0.1848       0.1686      0.1701       0.1693       0.4076       0.4174    0.1555        0.1581    0.1733    0.1744      0.1374    0.1631       0.1301       0.1208       0.1542       0.1816       0.0856    0.2027       0.2445       0.2039     0.1574       0.1593      0.2133    0.1470    0.1298       0.1658    0.1581       0.1427        0.2011      0.1253       0.2293       0.0000    0.1434        0.2798     0.1625    0.1803    0.2836       0.1660      0.2822       0.1570      0.1483        0.3983    0.1644    0.2797    0.1631    0.1233       0.2176       0.2014    0.1578        0.1433    0.2977     0.1108       0.2172       0.1918    0.3940\n",
       "Llama           0.1724       0.1559      0.1600       0.1578       0.4089       0.4160    0.1400        0.1502    0.1388    0.1614      0.1556    0.1504       0.1447       0.1409       0.1421       0.1734       0.1348    0.1903       0.2334       0.1908     0.1495       0.1532      0.1952    0.1141    0.1197       0.1583    0.1498       0.0979        0.1969      0.1371       0.2180       0.1434    0.0000        0.2620     0.1470    0.1697    0.2786       0.1602      0.2693       0.1495      0.1391        0.3973    0.1229    0.2740    0.1560    0.1142       0.2126       0.2297    0.1490        0.0999    0.2896     0.1460       0.2114       0.1778    0.3899\n",
       "Madagascar      0.2410       0.2388      0.2592       0.2395       0.4458       0.4407    0.2709        0.2599    0.2857    0.2829      0.2758    0.2216       0.2761       0.2706       0.2587       0.2795       0.2757    0.2961       0.2991       0.2420     0.2588       0.2517      0.3169    0.2696    0.2605       0.2613    0.2603       0.2635        0.2911      0.2740       0.2826       0.2798    0.2620        0.0000     0.2234    0.2844    0.3537       0.2643      0.3608       0.2618      0.2740        0.4391    0.2759    0.3506    0.2651    0.2529       0.2741       0.3299    0.2531        0.2650    0.1332     0.2783       0.2764       0.2854    0.4245\n",
       "Manatee         0.1144       0.0753      0.1363       0.0762       0.3905       0.3931    0.1563        0.1464    0.1823    0.1733      0.1632    0.0152       0.1534       0.1528       0.1344       0.1641       0.1543    0.1879       0.1881       0.1262     0.1460       0.1208      0.2037    0.1580    0.1351       0.1571    0.1492       0.1481        0.1865      0.1527       0.1632       0.1625    0.1470        0.2234     0.0000    0.1802    0.2685       0.1367      0.2703       0.1464      0.1478        0.3738    0.1661    0.2635    0.1508    0.1273       0.1332       0.2387    0.1292        0.1491    0.2466     0.1585       0.1323       0.1759    0.3715\n",
       "Mole            0.2045       0.1898      0.1929       0.1903       0.4175       0.4223    0.1793        0.1750    0.1955    0.1917      0.1831    0.1794       0.1794       0.1681       0.1718       0.1976       0.1693    0.2190       0.2605       0.2165     0.1757       0.1826      0.2113    0.1782    0.1553       0.1864    0.1778       0.1642        0.2181      0.1759       0.2461       0.1803    0.1697        0.2844     0.1802    0.0000    0.3087       0.1932      0.2976       0.1761      0.1720        0.4028    0.1876    0.3015    0.1830    0.1496       0.2345       0.2596    0.1831        0.1707    0.3102     0.1785       0.2347       0.1987    0.4008\n",
       "Mouse           0.2955       0.2898      0.2851       0.2891       0.4541       0.4560    0.2901        0.2556    0.2868    0.2989      0.2991    0.2686       0.2929       0.2884       0.2597       0.2616       0.2762    0.3021       0.3433       0.3069     0.2563       0.2740      0.3399    0.2718    0.2674       0.2666    0.2582       0.2783        0.2955      0.2793       0.3236       0.2836    0.2786        0.3537     0.2685    0.3087    0.0000       0.2825      0.3474       0.2563      0.2796        0.4525    0.2893    0.1133    0.2584    0.2709       0.3171       0.3405    0.2778        0.2794    0.3633     0.2948       0.3137       0.2874    0.4407\n",
       "NineBande       0.1634       0.1486      0.1134       0.1504       0.3916       0.3963    0.1669        0.1550    0.1878    0.1800      0.1718    0.1374       0.1681       0.1571       0.1381       0.1753       0.1617    0.1996       0.2267       0.1771     0.1553       0.0614      0.2230    0.1668    0.1482       0.1629    0.1575       0.1539        0.1921      0.1641       0.2151       0.1660    0.1602        0.2643     0.1367    0.1932    0.2825       0.0000      0.2774       0.1568      0.1637        0.3814    0.1751    0.2757    0.1598    0.1396       0.2003       0.2557    0.0971        0.1555    0.2867     0.1658       0.2007       0.1827    0.3741\n",
       "OldWorld        0.2960       0.2782      0.2774       0.2801       0.4654       0.4796    0.2817        0.2678    0.2967    0.2935      0.2937    0.2684       0.2858       0.2843       0.2594       0.2627       0.2769    0.3043       0.3485       0.3046     0.2667       0.2667      0.3357    0.2786    0.2660       0.2803    0.2686       0.2776        0.2935      0.2760       0.3394       0.2822    0.2693        0.3608     0.2703    0.2976    0.3474       0.2774      0.0000       0.2675      0.2826        0.4547    0.2850    0.3407    0.2714    0.2650       0.3167       0.3235    0.2719        0.2764    0.3694     0.2886       0.3189       0.3104    0.4498\n",
       "Orangutan       0.1708       0.1552      0.1577       0.1563       0.4028       0.4076    0.1605        0.0137    0.1801    0.1737      0.1695    0.1468       0.1598       0.1551       0.1259       0.1552       0.1523    0.1681       0.2444       0.1896     0.0134       0.1444      0.2160    0.1598    0.1399       0.0679    0.0173       0.1498        0.1841      0.1563       0.2157       0.1570    0.1495        0.2618     0.1464    0.1761    0.2563       0.1568      0.2675       0.0000      0.1527        0.3886    0.1677    0.2528    0.0395    0.1331       0.2044       0.2427    0.1520        0.1487    0.2838     0.1651       0.2037       0.1683    0.3855\n",
       "Pangolin        0.1788       0.1625      0.1608       0.1622       0.4114       0.4178    0.1354        0.1531    0.1651    0.1599      0.1498    0.1508       0.1411       0.1377       0.1377       0.1671       0.1365    0.1967       0.2434       0.1910     0.1534       0.1491      0.2032    0.1440    0.1195       0.1627    0.1538       0.1267        0.1933      0.1397       0.2226       0.1483    0.1391        0.2740     0.1478    0.1720    0.2796       0.1637      0.2826       0.1527      0.0000        0.4003    0.1517    0.2746    0.1597    0.1153       0.2164       0.2366    0.1578        0.1293    0.2970     0.1405       0.2134       0.1790    0.3875\n",
       "Phascogale      0.3896       0.3798      0.3894       0.3798       0.1828       0.2004    0.3951        0.3881    0.4114    0.4025      0.4088    0.3722       0.4121       0.4010       0.3819       0.4014       0.4001    0.4048       0.4164       0.3983     0.3894       0.3799      0.4186    0.4037    0.3820       0.3990    0.3903       0.3966        0.4050      0.4028       0.4025       0.3983    0.3973        0.4391     0.3738    0.4028    0.4525       0.3814      0.4547       0.3886      0.4003        0.0000    0.4033    0.4485    0.3934    0.3833       0.4007       0.4492    0.3799        0.4016    0.4537     0.4005       0.4023       0.3872    0.1358\n",
       "Pig             0.1914       0.1806      0.1767       0.1818       0.4137       0.4232    0.1620        0.1688    0.1499    0.1804      0.1687    0.1656       0.1613       0.1540       0.1538       0.1885       0.1517    0.2154       0.2513       0.2080     0.1681       0.1653      0.2199    0.1224    0.1411       0.1812    0.1699       0.1065        0.2082      0.1528       0.2305       0.1644    0.1229        0.2759     0.1661    0.1876    0.2893       0.1751      0.2850       0.1677      0.1517        0.4033    0.0000    0.2888    0.1807    0.1348       0.2270       0.2404    0.1695        0.1073    0.2941     0.1566       0.2266       0.2004    0.3938\n",
       "Rat             0.2902       0.2800      0.2779       0.2792       0.4515       0.4502    0.2797        0.2532    0.2877    0.2878      0.2899    0.2644       0.2833       0.2805       0.2549       0.2563       0.2719    0.2928       0.3368       0.2955     0.2532       0.2639      0.3307    0.2709    0.2606       0.2631    0.2550       0.2752        0.2852      0.2747       0.3180       0.2797    0.2740        0.3506     0.2635    0.3015    0.1133       0.2757      0.3407       0.2528      0.2746        0.4485    0.2888    0.0000    0.2583    0.2619       0.3091       0.3439    0.2721        0.2770    0.3610     0.2915       0.3079       0.2841    0.4382\n",
       "Rhesus          0.1775       0.1604      0.1614       0.1612       0.4093       0.4120    0.1667        0.0381    0.1896    0.1813      0.1749    0.1513       0.1664       0.1584       0.1275       0.1582       0.1600    0.1697       0.2490       0.1946     0.0378       0.1482      0.2151    0.1682    0.1479       0.0690    0.0410       0.1564        0.1871      0.1636       0.2238       0.1631    0.1560        0.2651     0.1508    0.1830    0.2584       0.1598      0.2714       0.0395      0.1597        0.3934    0.1807    0.2583    0.0000    0.1374       0.2123       0.2460    0.1572        0.1564    0.2896     0.1675       0.2112       0.1700    0.3899\n",
       "Rhino           0.1542       0.1406      0.1388       0.1403       0.3997       0.4049    0.1216        0.1320    0.1480    0.1360      0.1279    0.1298       0.1210       0.1134       0.1164       0.1544       0.1119    0.1750       0.2170       0.1754     0.1316       0.1281      0.1829    0.1197    0.0729       0.1454    0.1338       0.1084        0.1745      0.1155       0.2021       0.1233    0.1142        0.2529     0.1273    0.1496    0.2709       0.1396      0.2650       0.1331      0.1153        0.3833    0.1348    0.2619    0.1374    0.0000       0.1924       0.2036    0.1321        0.1117    0.2746     0.1200       0.1917       0.1604    0.3790\n",
       "RockHyrax       0.1726       0.1414      0.2020       0.1418       0.4163       0.4196    0.2167        0.2055    0.2375    0.2257      0.2190    0.1310       0.2177       0.2054       0.1914       0.2165       0.2085    0.2395       0.2435       0.1945     0.2059       0.1844      0.2575    0.2210    0.2007       0.2126    0.2085       0.2118        0.2355      0.2114       0.2224       0.2176    0.2126        0.2741     0.1332    0.2345    0.3171       0.2003      0.3167       0.2044      0.2164        0.4007    0.2270    0.3091    0.2123    0.1924       0.0000       0.2879    0.1911        0.2158    0.3009     0.2145       0.0135       0.2325    0.4037\n",
       "RoundEare       0.2596       0.2434      0.2471       0.2442       0.4497       0.4592    0.2400        0.2419    0.2555    0.2560      0.2203    0.2360       0.2234       0.2112       0.2362       0.2530       0.1975    0.2840       0.3184       0.2832     0.2408       0.2461      0.2852    0.2341    0.2124       0.2459    0.2434       0.2301        0.2652      0.2121       0.3012       0.2014    0.2297        0.3299     0.2387    0.2596    0.3405       0.2557      0.3235       0.2427      0.2366        0.4492    0.2404    0.3439    0.2460    0.2036       0.2879       0.0000    0.2402        0.2285    0.3451     0.1964       0.2875       0.2651    0.4361\n",
       "Sloth           0.1529       0.1418      0.0934       0.1425       0.3904       0.3991    0.1582        0.1499    0.1784    0.1736      0.1604    0.1299       0.1664       0.1486       0.1318       0.1686       0.1483    0.1909       0.2206       0.1712     0.1506       0.0853      0.2148    0.1608    0.1418       0.1609    0.1524       0.1452        0.1879      0.1557       0.2073       0.1578    0.1490        0.2531     0.1292    0.1831    0.2778       0.0971      0.2719       0.1520      0.1578        0.3799    0.1695    0.2721    0.1572    0.1321       0.1911       0.2402    0.0000        0.1497    0.2775     0.1545       0.1919       0.1780    0.3746\n",
       "SpermWhale      0.1788       0.1619      0.1550       0.1635       0.4171       0.4234    0.1391        0.1484    0.1124    0.1636      0.1474    0.1492       0.1398       0.1351       0.1374       0.1740       0.1315    0.1917       0.2308       0.1933     0.1484       0.1463      0.1985    0.0817    0.1183       0.1587    0.1477       0.0254        0.1917      0.1326       0.2179       0.1433    0.0999        0.2650     0.1491    0.1707    0.2794       0.1555      0.2764       0.1487      0.1293        0.4016    0.1073    0.2770    0.1564    0.1117       0.2158       0.2285    0.1497        0.0000    0.2845     0.1404       0.2147       0.1772    0.3961\n",
       "Tenrec          0.2696       0.2559      0.2816       0.2558       0.4609       0.4598    0.2894        0.2823    0.3031    0.3037      0.3061    0.2449       0.3034       0.2965       0.2737       0.3014       0.2960    0.3216       0.3198       0.2626     0.2812       0.2730      0.3335    0.2868    0.2770       0.2903    0.2845       0.2848        0.3101      0.2952       0.3009       0.2977    0.2896        0.1332     0.2466    0.3102    0.3633       0.2867      0.3694       0.2838      0.2970        0.4537    0.2941    0.3610    0.2896    0.2746       0.3009       0.3451    0.2775        0.2845    0.0000     0.2993       0.3024       0.3042    0.4385\n",
       "TombBat         0.1808       0.1677      0.1672       0.1685       0.4062       0.4232    0.1482        0.1622    0.1743    0.1659      0.1361    0.1586       0.1333       0.1245       0.1450       0.1738       0.0956    0.2009       0.2396       0.2034     0.1622       0.1571      0.2051    0.1520    0.1299       0.1677    0.1640       0.1392        0.1950      0.1272       0.2245       0.1108    0.1460        0.2783     0.1585    0.1785    0.2948       0.1658      0.2886       0.1651      0.1405        0.4005    0.1566    0.2915    0.1675    0.1200       0.2145       0.1964    0.1545        0.1404    0.2993     0.0000       0.2114       0.1898    0.3926\n",
       "TreeHyrax       0.1741       0.1409      0.2006       0.1412       0.4165       0.4211    0.2152        0.2041    0.2378    0.2245      0.2171    0.1302       0.2172       0.2059       0.1893       0.2168       0.2074    0.2394       0.2445       0.1949     0.2044       0.1834      0.2570    0.2213    0.1985       0.2103    0.2066       0.2106        0.2351      0.2095       0.2242       0.2172    0.2114        0.2764     0.1323    0.2347    0.3137       0.2007      0.3189       0.2037      0.2134        0.4023    0.2266    0.3079    0.2112    0.1917       0.0135       0.2875    0.1919        0.2147    0.3024     0.2114       0.0000       0.2312    0.4052\n",
       "TreeShrew       0.1983       0.1848      0.1851       0.1867       0.4024       0.4070    0.1816        0.1632    0.2010    0.2016      0.1942    0.1739       0.1966       0.1814       0.1573       0.1836       0.1824    0.1953       0.2513       0.2134     0.1646       0.1675      0.2351    0.1867    0.1697       0.1798    0.1680       0.1753        0.2042      0.1914       0.2328       0.1918    0.1778        0.2854     0.1759    0.1987    0.2874       0.1827      0.3104       0.1683      0.1790        0.3872    0.2004    0.2841    0.1700    0.1604       0.2325       0.2651    0.1780        0.1772    0.3042     0.1898       0.2312       0.0000    0.3834\n",
       "Wombat          0.3888       0.3758      0.3806       0.3758       0.1503       0.1740    0.3914        0.3831    0.4039    0.3962      0.4018    0.3684       0.4035       0.3916       0.3786       0.3956       0.3899    0.3976       0.4157       0.3943     0.3831       0.3720      0.4192    0.3976    0.3771       0.3934    0.3882       0.3928        0.4053      0.3911       0.3950       0.3940    0.3899        0.4245     0.3715    0.4008    0.4407       0.3741      0.4498       0.3855      0.3875        0.1358    0.3938    0.4382    0.3899    0.3790       0.4037       0.4361    0.3746        0.3961    0.4385     0.3926       0.4052       0.3834    0.0000\n",
       "---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pair_distance = aln.distance_matrix()\n",
    "pair_distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "seq_coll = aln.degap()\n",
    "data = seq_coll.to_dict()  #get unaligned sequences collection"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Plot out the error between co-distance and fractional difference"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "dcos = pair_dco(seq_coll=data, pair_distance=pair_distance, k=19,context_len=9,obj_len=1)\n",
    "length_diff = pair_len_diff(data, pair_distance)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "num_seqs = pair_distance.shape[0]\n",
    "indices = numpy.tril_indices(num_seqs)\n",
    "\n",
    "dcos = dcos[indices]\n",
    "frac_diff = pair_distance.array[indices] \n",
    "length_diff = length_diff[indices]\n",
    "errors = dcos - frac_diff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
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           "zerolinecolor": "white",
           "zerolinewidth": 2
          }
         }
        },
        "title": {
         "text": "Errors v.s. absolute length difference <br>data without gaps; `length of C_gram` = 18, `length of O_gram` = 1."
        },
        "xaxis": {
         "anchor": "y",
         "domain": [
          0,
          1
         ],
         "title": {
          "text": "absolute difference in length"
         }
        },
        "yaxis": {
         "anchor": "x",
         "domain": [
          0,
          1
         ],
         "title": {
          "text": "co_distance - fraction_diff"
         }
        }
       }
      }
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "fig = px.scatter(x=length_diff, y=errors,\n",
    "    labels={\"x\": \"absolute difference in length\", \"y\": \"co_distance - fraction_diff\"}, \n",
    "    title = \"Errors v.s. absolute length difference <br>data without gaps; `length of C_gram` = 18, `length of O_gram` = 1.\")\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
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    "    title = \"Comparison between co_distance and fractional difference <br>data without gaps `length of C_gram` = 18, `length of O_gram` = 1.\")\n",
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