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# Building alignments

## Using a `cogent3` progressive aligner for nucleotides

We load a canned nucleotide substitution model and the progressive aligner `tree_align` function.

We first align without providing a guide tree. The `tree_align` algorithm builds pairwise alignments and estimates the substitution model parameters and pairwise distances. The distances are used to build a neighbour joining tree and the median value of substitution model parameters are provided to the substitution model for the progressive alignment step.

We then align using a guide tree (pre-estimated) and specifying the ratio of transitions to transversions (kappa).

## Using a `cogent3` progressive aligner for codons

We load a canned codon substitution model and use a pre-defined tree and parameter estimates.

## Converting gaps from aa-seq alignment to nuc seq alignment

We load some unaligned DNA sequences and show their translation.

We load an alignment of these protein sequences.

We then obtain an alignment of the DNA sequences by aligning their translations.