Find the evolutionary tree or trees that best accounts for the
observed variation (mismatches) in the multiple alignment of a group
of sequences.
Methods:
[few sequences, low variation]
- Character based: Maximum parsimony, compatibility
- Distance based: Neighbour-joining, UPGMA
- Probabilistic approaches: Maximum likelihood
[many sequences, high variation]
| #species | #rooted | #unrooted |
| 3 | 3 | 1 |
| 4 | 15 | 3 |
| 5 | 105 | 15 |
| 10 | 34459425 | 2027025 |
For n species, there are 1 x 3 x 5 x ... x (2n - 3) rooted trees
Bootstrap analysis of trees:
Reliability of a predicted phylogenetic tree.
- Resampling data by random selection of columns in the msa to create a new one
- Compute the phylogenetic tree with the same method
- Significant branches should frequently appear in the resampled trees
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