Package index
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define_growth_curve() - Define active infected cell growth curve
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define_sampling_scheme() - Define sampling scheme
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slice_aln() - Slice alignment
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extract_seqs() - Extract founder (and reference) sequence from an alignment
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estimate_q() - Calculate nucleotide substitution probabilities
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calc_q_from_rates() - Calculate Q matrix from nucleotide substitution rates
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identify_conserved_sites() - Identify conserved sites
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get_epitope_frequencies() - Get epitope frequencies
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sample_epitopes() - Sample epitopes
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map_ref_founder() - Map reference and founder sequence positions
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create_python_venv() - Create python virtual environment and dependencies in conda or virtualenv environment
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remove_python_venv() - Uninstall the wavess environment
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run_wavess() - Run wavess
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calc_div_metrics() - Calculate sequence-based diversity and divergence
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calc_tr_stats() - Calculate tree summary statistics
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hxb2_cons_founder - HXB2, consensus, and founder alignment
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hiv_mut_rates - HIV nucleotide-specific mutation rates at approximately neutral sites
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founder_conserved_sites - Example founder conserved sites
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hiv_env_flt_2022 - HIV1 ENV alignment
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env_features - ENV features