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EllaSantanaPropperGreg Caporaso
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Update phylogeny-reconstruction.md (#309)
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book/fundamentals/phylogeny-reconstruction.md

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@@ -435,15 +435,15 @@ Step 3: We'll now fill in the values from the new clade to each of the existing
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```python
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>>> s2_s1s3 = np.mean([master_upgma_dm[1][0], master_upgma_dm[1][2]])
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>>> s3s4_s1s3 = np.mean([master_upgma_dm[0][3], master_upgma_dm[0][4], master_upgma_dm[2][3], master_upgma_dm[2][4]])
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>>> s4s5_s1s3 = np.mean([master_upgma_dm[0][3], master_upgma_dm[0][4], master_upgma_dm[2][3], master_upgma_dm[2][4]])
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```
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We can now fill in all of the distances in our iteration 2 distance matrix.
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```python
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>>> iter2_dm = [[0.0, s2_s1s3, s3s4_s1s3],
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>>> iter2_dm = [[0.0, s2_s1s3, s4s5_s1s3],
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... [s2_s1s3, 0.0, 5.5],
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... [s3s4_s1s3, 5.5, 0.0]]
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... [s4s5_s1s3, 5.5, 0.0]]
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...
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>>> iter2_dm = DistanceMatrix(iter2_dm, iter2_ids)
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>>> print(iter2_dm)

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