├── .gitignore ├── .travis.yml ├── CODE-OF-CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile.template ├── ISSUE_TEMPLATE.md ├── LICENSE ├── README.md ├── book ├── applications │ ├── biological-diversity.md │ ├── images │ │ ├── basic-unrooted-tree1.jpg │ │ ├── example_big_dm.png │ │ ├── unifrac_tree_d0.5.graffle │ │ ├── unifrac_tree_d0.5.png │ │ ├── unifrac_tree_d0.graffle │ │ ├── unifrac_tree_d0.png │ │ ├── unifrac_tree_d1.graffle │ │ ├── unifrac_tree_d1.png │ │ ├── unifrac_tree_with_distances.graffle │ │ ├── unifrac_tree_with_distances.png │ │ ├── unifrac_tree_with_distances_ab.graffle │ │ └── unifrac_tree_with_distances_ab.png │ ├── index.md │ └── index.yaml ├── back-matter │ ├── about-the-author.md │ ├── glossary.md │ ├── index.md │ └── index.yaml ├── config.yaml ├── exercises │ ├── index.md │ ├── index.yaml │ ├── multiple-sequence-alignment.md │ └── pairwise-alignment.md ├── fundamentals │ ├── database-searching.md │ ├── images │ │ ├── Darwins_tree_of_life_1859.png │ │ ├── Pace_Big_Tree.png │ │ ├── alignment.graffle │ │ ├── alignment.png │ │ ├── basic-rooted-tree1.jpg │ │ ├── basic-unrooted-tree1.jpg │ │ ├── centroid-cluster.1.png │ │ ├── centroid-cluster.2.png │ │ ├── centroid-cluster.3.png │ │ ├── centroid-cluster.4.png │ │ ├── centroid-cluster.5.png │ │ ├── centroid-cluster.6.png │ │ ├── centroid-cluster.graffle │ │ ├── cluster-legend.graffle │ │ ├── cluster-legend.png │ │ ├── cluster-template.graffle │ │ │ ├── data.plist │ │ │ └── image1.pdf │ │ ├── cluster-types.graffle │ │ │ ├── data.plist │ │ │ └── image2.pdf │ │ ├── cluster-types.png │ │ ├── furthest-neighbor.1.png │ │ ├── furthest-neighbor.2.png │ │ ├── furthest-neighbor.3.png │ │ ├── furthest-neighbor.4.png │ │ ├── furthest-neighbor.5.png │ │ ├── furthest-neighbor.6.png │ │ ├── furthest-neighbor.graffle │ │ │ ├── data.plist │ │ │ └── image1.pdf │ │ ├── msa-tree-a1.graffle │ │ ├── msa-tree-a1.png │ │ ├── msa-tree-a2.graffle │ │ ├── msa-tree-a2.png │ │ ├── msa-tree-a3.graffle │ │ ├── msa-tree-a3.png │ │ ├── msa-tree-final.graffle │ │ ├── msa-tree-final.png │ │ ├── msa-tree-input.graffle │ │ ├── msa-tree-input.png │ │ ├── nearest-neighbor.1.png │ │ ├── nearest-neighbor.2.png │ │ ├── nearest-neighbor.3.png │ │ ├── nearest-neighbor.4.png │ │ ├── nearest-neighbor.5.png │ │ ├── nearest-neighbor.6.png │ │ ├── nearest-neighbor.graffle │ │ ├── sequence-evo-tree.graffle │ │ ├── sequence-evo-tree.png │ │ ├── spider-tree.png │ │ ├── tree-monophyly.graffle │ │ ├── tree-monophyly.png │ │ ├── tree-polyphyly.graffle │ │ ├── tree-polyphyly.png │ │ ├── tree-schematic1.graffle │ │ ├── tree-schematic1.png │ │ ├── upgma-tree-final.graffle │ │ ├── upgma-tree-final.png │ │ ├── upgma-tree-iter1.graffle │ │ ├── upgma-tree-iter1.png │ │ ├── upgma-tree-iter2.graffle │ │ ├── upgma-tree-iter2.png │ │ ├── upgma-tree-iter3.graffle │ │ └── upgma-tree-iter3.png │ ├── index.md │ ├── index.yaml │ ├── machine-learning.md │ ├── multiple-sequence-alignment.md │ ├── pairwise-alignment.md │ ├── phylogeny-reconstruction.md │ └── sequence-mapping-and-clustering.md ├── getting-started │ ├── biological-information.md │ ├── images │ │ ├── central-dogma.png │ │ ├── genetic-code.png │ │ ├── greg-in-telluride.png │ │ └── trna.png │ ├── index.md │ ├── index.yaml │ └── reading-iab.md ├── images │ └── logo.png ├── index.md └── index.yaml ├── custom.css ├── environment.yml ├── iab ├── __init__.py ├── algorithms │ └── __init__.py ├── data │ └── __init__.py └── format │ ├── __init__.py │ └── dialog_box.py ├── licenses ├── runipy.txt └── scikit-bio.txt ├── paper.bib ├── paper.md ├── runipynbs.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/applied-bioinformatics/An-Introduction-To-Applied-Bioinformatics/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 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