I calculated a pairwise distance matrix in ClustalO. The distances are between 16s sequences after pairwise alignment.
The problem is, that the distance matrix is not quadratic (2388x2196 -> more rows than columns) and I can not find out why from the data without extensively crawling through the output text file.
Does anyone know?
Additional info: Clustal says the following:
*************************************************
Read 2195 sequences (type: DNA) from /path/subs.fa
Calculating pairwise ktuple-distances...
Pairwise distance matrix written to distMat(2386081 out of 2410110)
Ktuple-distance calculation progress done. CPU time: 560.17u 22.48s 00:09:42.65 Elapsed: 00:05:42
Guide-tree computation done.
Progressive alignment progress done. CPU time: 396.45u 0.65s 00:06:37.10 Elapsed: 00:06:38
The problem is, that the distance matrix is not quadratic (2388x2196 -> more rows than columns) and I can not find out why from the data without extensively crawling through the output text file.
Does anyone know?
Additional info: Clustal says the following:
*************************************************
Read 2195 sequences (type: DNA) from /path/subs.fa
Calculating pairwise ktuple-distances...
Pairwise distance matrix written to distMat(2386081 out of 2410110)
Ktuple-distance calculation progress done. CPU time: 560.17u 22.48s 00:09:42.65 Elapsed: 00:05:42
Guide-tree computation done.
Progressive alignment progress done. CPU time: 396.45u 0.65s 00:06:37.10 Elapsed: 00:06:38
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