What format does the MSA data need to be in order to calculate pair-wise distances with seqpdist?
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I am reading a clustalw text format msa with multialignread. I have tried splitting the msaread data into two cells, and keeping the structure in tact, neither method has been successful. Seqpdist does accept the sequence cell output of fastaread fasta text file of the same sequences. %This works... [heads,seqs]=fastaread('fastaformat.fasta'); distancematrix=seqpdist(seqs,'method',pam(250),'squareform',1); %This does not... [heads,seqs]=multialignread('clustalwmsa.aln1'); distancematrix=seqpdist(seqs,'method',pam(250),'squareform',1);
This is the error message:
??? Error using ==> cell.strmatch at 21
Requires character array or cell array of strings as inputs.
Error in ==> seqpdist at 258
distMethod = strmatch(lower(pval),distMethods);
Error in ==> cscalc at 14
dmat=seqpdist(seqs,'method',pam(250),'squareform',1);
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Walter Roberson
am 11 Jun. 2011
What you pass for 'method' must be a string.
The reference to pam appears to be something appropriate for a 'ScoringMatrix' parameter and the parameter you would pass for that would be the string 'pam250'
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