Compute a identity matrix from an alignment - command line approach for batch processing

Question

[fhsantanna]

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?

[Brian Bushnell]

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.

Answer 1

[Michael]

DNA or AA? Otherwise, computing a distance matrix on MSA is a basic task in phylogenetics, done - for example - by long-existing tools:

• Protdist
• DNAdist

• Gendist

  in Phylip, see http://evolution.genetics.washington.edu/phylip/progs.data.dist.html

EMBOSS: distmat

MEGA can also calculate distance matrices.

[fhsantanna]

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.

[Michael]

So, what do you want to calculate:

1. For each pair, the number of identical positions
2. the proportion of identical values (% identity)
3. the actual sequences that are identical

[fhsantanna]

I would like to compute the % identity.

Answer 2

[gadget]

See PIM from MUSCLE