Merge pull request #90 from gregcaporaso/issue-17

update notebook file names and corresponding links

Author: Greg Caporaso

Index.ipynb

@@ -1,7 +1,7 @@
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@@ -60,15 +60,23 @@
      "source": [
       "0. [Getting started](getting-started/Index.ipynb): using the IPython Notebook and *An Introduction To Applied Bioinformatics*\n",
       "1. Fundamentals\n",
-      "  1. [Pairwise alignment](algorithms/1-pairwise-alignment.ipynb) ([exercise](algorithms/pairwise-alignment-exercises.ipynb))\n",
-      "  2. [Database searching and determining the statistical significance of an alignment](algorithms/2-database-searching.ipynb)\n",
-      "  3. [Phylogeny reconstruction: distances, distances matrices and hierarchical clustering with UPGMA](algorithms/3-phylogeny-reconstruction.ipynb)\n",
-      "  4. [Multiple sequence alignment](algorithms/4-multiple-sequence-alignment.ipynb) ([exercise](algorithms/msa-assignment.ipynb))\n",
-      "  5. [Read mapping and clustering](algorithms/5-sequence-mapping-and-clustering.ipynb?create=1)\n",
+      "  1. [Pairwise alignment](fundamentals/pairwise-alignment.ipynb) ([exercise](fundamentals/pairwise-alignment-exercises.ipynb))\n",
+      "  2. [Database searching and determining the statistical significance of an alignment](fundamentals/database-searching.ipynb)\n",
+      "  3. [Phylogeny reconstruction: distances, distances matrices and hierarchical clustering with UPGMA](fundamentals/phylogeny-reconstruction.ipynb)\n",
+      "  4. [Multiple sequence alignment](fundamentals/multiple-sequence-alignment.ipynb) ([exercise](fundamentals/msa-assignment.ipynb))\n",
+      "  5. [Read mapping and clustering](fundamentals/sequence-mapping-and-clustering.ipynb?create=1)\n",
       "2. Applications\n",
-      "  1. [Studying biological diversity](applications/1-biological-diversity.ipynb)\n",
+      "  1. [Studying biological diversity](applications/biological-diversity.ipynb)\n",
       "3. Wrapping up"
      ]
+    },
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+     "input": [],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
     }
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    "metadata": {}