##############
Usage Examples
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*****************
Data manipulation
*****************

.. toctree::
    :maxdepth: 1

    translate_dna
    seq_features
    complete_seq_features
    reverse_complement
    align_codons_to_protein
    handling_tabular_data
    manipulating_tree_nodes

*********************
General data analysis
*********************

.. toctree::
    :maxdepth: 1

    period_estimation

*******************
Modelling Evolution
*******************

.. toctree::
    :maxdepth: 1

    simple
    relative_rate
    neutral_test
    scope_model_params_on_trees
    codon_models
    empirical_protein_models
    testing_multi_loci
    simulate_alignment
    parametric_bootstrap
    coevolution
    rate_heterogeneity
    hmm_par_heterogeneity

***************************
Phylogenetic Reconstruction
***************************

.. toctree::
    :maxdepth: 1

    calculate_pairwise_distances
    calculate_neigbourjoining_tree
    calculate_UPGMA_cluster
    phylo_by_ls
    maketree_from_proteinseqs