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Ancestral sequence reconstruction using TreeTime
------------------------------------------------
At the core of TreeTime is a class that models how sequences change along the tree.
This class allows to reconstruct likely sequences of internal nodes of the tree.
On the command-line, ancestral reconstruction can be done via the command
.. code-block:: bash
treetime ancestral --aln data/h3n2_na/h3n2_na_20.fasta --tree data/h3n2_na/h3n2_na_20.nwk --outdir ancestral_results
This command will save a number of files into the directory `ancestral_results` and generate the output
.. code-block:: bash
Inferred GTR model:
Substitution rate (mu): 1.0
Equilibrium frequencies (pi_i):
A: 0.2983
C: 0.1986
G: 0.2353
T: 0.2579
-: 0.01
Symmetrized rates from j->i (W_ij):
A C G T -
A 0 0.8273 2.8038 0.4525 1.031
C 0.8273 0 0.5688 2.8435 1.0561
G 2.8038 0.5688 0 0.6088 1.0462
T 0.4525 2.8435 0.6088 0 1.0418
- 1.031 1.0561 1.0462 1.0418 0
Actual rates from j->i (Q_ij):
A C G T -
A 0 0.2468 0.8363 0.135 0.3075
C 0.1643 0 0.1129 0.5646 0.2097
G 0.6597 0.1338 0 0.1432 0.2462
T 0.1167 0.7332 0.157 0 0.2686
- 0.0103 0.0106 0.0105 0.0104 0
--- alignment including ancestral nodes saved as
ancestral_results/ancestral_sequences.fasta
--- tree saved in nexus format as
ancestral_results/annotated_tree.nexus
TreeTime has inferred a GTR model and used it to reconstruct the most likely ancestral sequences.
The reconstructed sequences will be written to a file ending in ``_ancestral.fasta`` and a tree with mutations mapped to branches will be saved in nexus format in a file ending on ``_mutation.nexus``.
Mutations are added as comments to the nexus file like ``[&mutations="G27A,A58G,A745G,G787A,C1155T,G1247A,G1272A"]``.
Amino acid sequences
^^^^^^^^^^^^^^^^^^^^
Ancestral reconstruction of amino acid sequences works analogously to nucleotide sequences.
However, the user has to either explicitly choose an amino acid substitution model (JTT92)
.. code-block:: bash
treetime ancestral --tree data/h3n2_na/h3n2_na_20.nwk --aln data/h3n2_na/h3n2_na_20_aa.fasta --gtr JTT92
or specify that this is a protein sequence alignment using the flag ``--aa``\ :
.. code-block:: bash
treetime ancestral --tree data/h3n2_na/h3n2_na_20.nwk --aln data/h3n2_na/h3n2_na_20_aa.fasta --aa
VCF files as input
^^^^^^^^^^^^^^^^^^
In addition to standard fasta files, TreeTime can ingest sequence data in form of vcf files which is common for bacterial data sets where short reads are mapped against a reference and only variable sites are reported.
In this case, an additional argument specifying the mapping reference is required.
.. code-block:: bash
treetime ancestral --aln data/tb/lee_2015.vcf.gz --vcf-reference data/tb/tb_ref.fasta --tree data/tb/lee_2015.nwk
The ancestral reconstruction is saved as a vcf files with the name ``ancestral_sequences.vcf``.
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