Distance matrix with different length sequences - novice question
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7.2 years ago
mootzk • 0

Hi all,

Real beginner here, so be gentle :)

In a project we're doing (in python), we want to create a distance matrix for a phylogenetic tree with multiple, different length sequences. However, what we've seen so far (AlignIO in biopython, etc.) requires the sequences' length to be equal. Is there any python-ian way to get the matrix with sequences of different length? Or any other indirect way that would get us to the same result.

Thanks,

Nir

distance matrix • 1.5k views
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Entering edit mode
7.2 years ago
David W 4.8k

You will have to align your sequences before you can make a tree. The biopython tutorial has quite a few examples of how to script sequence alignment  programs, and there are hundreds of general introductions to sequence alignment.

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