Sample an alignment to a fixed length

Let’s load in an alignment of rodents to use in the examples.

How to sample the first n positions of an alignment

We can use the fixed_length app to sample an alignment to a fixed length. By default, it will sample from the beginning of an alignment, the argument length=20 specifies how many positions to sample.

How to sample n positions from within an alignment

Creating the fixed_length app with the argument start=x specifies that the sampled sequence should begin x positions into the alignment.

How to sample n positions randomly from within an alignment

The start position can be selected at random with random=True. An optional seed can be provided to ensure the same start position is used when the app is called.