Create distance matrix object from input alignment in BioPython
In Biopython, is there a way to create a distance matrix (i.e. a distance matrix 'object' that could be read and manipulated), using an alignment as input?
The "distancematrix" method in Bio.Cluster is giving me problems (ValueError: data has incorrect rank (1 expected 2)) when reading in an alignment file using Cluster.read(), and it won't accept a Numpy array either.
I realize there there is likely an easy solution to this problem, but I've spent the better part of today trying to find an easy way to even calculate the distance between two aligned, amino acid sequences using Biopython.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Pairwise Sequence Alignments with Numbered Antibody Sequences
written by jsweet6 •
-
Extract sequence subset from multiple sequence alignment based on position in a specific species.
written by nad7wf •
-
obstain 100-way alignment of 100 species for a certain gene
written by qwzhang0601
-
Multiple alignment to matrix generation
written by mdsiddra •
-
Clustering biological sequences based on numeric values
written by keshavmot2 •
-
How do matrix weights for amino acid 'X' affect protein alignments in MUSCLE?
written by rleach
-
Ambiguous Amino Acid In Motif Search
written by jzabilansky •
-
Compute Affinity Matrix From Distance Matrix
written by ericmajinglong
-
Mouse Protein Homologs Of 380 Drosophila Genes
written by supernate88 •
-
Single Position Highlight In Multiple Sequence Alignment
written by Kamila001
I think we have an open issue on better distance matrix support on the old (RedMine) Biopython issue tracker, but that is currently offline, probably https://redmine.open-bio.org/issues/2034 (link not tested). See also http://lists.open-bio.org/pipermail/biopython/2006-June/003107.html