[Biopython] Bio.pairwise2

[Vitoria Zanon]

Hello! I hope this email finds you well.

My name is Vitoria and I'm currently using Biopython to develop a new
multiple sequence alignment tool as my PhD project, specially the
Bio.pairwise2 method, which is the main reason I'm writing this email: the
deprecated warning told me I should talk to you about this.

In my code, the pairwise2 method helps produce an alignment library which
contains *(n²-n)/2* pairwise alignments, being *n* the number of sequences
in the input file. This library helps the COFFEE objective function
<https://doi.org/10.1093/bioinformatics/14.5.407> (NOTREDAME et al., 1998)
to evaluate the MSAs produced by the tool. I was using the
Bio.Align.PairwiseAlignment method but I faced an issue with it: I couldn't
get the aligned sequences from the PairwiseAlignment object as a Seq
object, String or neither a SeqRecord object. The library should keep the
name of the sequences, the sequences itself and the alignment score, but
all I was able to do is to get the target/query sequences (unaligned) or
the Align object itself, which wouldn't work for me. However with pairwise2
i was able to get the sequences and work with them as i planned to. I must
admit the PairwiseAlignment has a more intuitive and useful class structure
and I already thought about using it in other projects from our lab, but it
doesn't work for this specific project in specific. I'm also sending a
print from my code to illustrate the pairwise2 use.

Therefore, I would like you to consider adding this feature in
PairwiseAlignment or as a different method since you discontinued
pairwise2. By now, my main objective is to finish the whole tool and test
its results so I can get data about the performance of the new algorithm
I'm proposing. After that I plan to make the tool available on the internet
and I want to work with the latest releases from each library involved so
it can work fine in any machine and improve its execution when the
libraries themselves get improved.

Thank you for reading!

Sincerely yours,
Vitoria
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