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Inferring phylogenetic relationships

Goals:

Reconstruct phylogenetic tree from homologous molecular sequences

Why:

Phylogenetic trees can help testing of various biological hypotheses, untangling the evolutionary history of sequences.
Phylogeny reconstruction can also be necessary for further analyses, such as detecting positive selection or clustering of sequences to study the evolution of other characteristics associated with sampled sequences.

Input data:

homologous multiple sequences (unaligned or aligned) in one of standard formats

Pipeline:

1. Align if not aligned.
2. Select model
3. Infer phylogeny method 1
4. Infer phylogeny method 1
5. Evaluate statistical uncertainty of phylogenies and branches
6. If needed, use other methods for steps 3-4.

Deliverables:

Newick tree or several best trees, with branch lengths and statistical supports.
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