I have an 16S rDNA alignment in FASTA format and I want to generate an identity matrix from it. Bioedit has a tool for this purpose, however I need a command line one for batch processing. Do you know a script able of doing it?
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fhsantanna
DNA or AA? Otherwise, computing a distance matrix on MSA is a basic task in phylogenetics, done - for example - by long-existing tools:
Gendist
in Phylip, see http://evolution.genetics.washington.edu/phylip/progs.data.dist.html
EMBOSS: distmat
MEGA can also calculate distance matrices.
Actually I need the opposite. Emboss and DNAdist calculate the distance. I just need the identity values among the sequences. I am working with rRNA 16S sequences, and their identity values are important for bacterial species identification.
So, what do you want to calculate:
I would like to compute the % identity.
See PIM from MUSCLE
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It might be helpful if you described the problem in more detail. For example - "I have hundreds of alignments and I want to generate an identity matrix for each one of them"
This does not have the necessary information. Do you mean that you have hundreds of files? One file with lots of alignments? What is the format of your alignments? ...etc. So, please clarify.