What it does
cmalign aligns the RNA sequences to the covariance model (CM).
The sequence file must be in FASTA or Genbank format. cmalign uses an HMM banding technique to accelerate alignment by default. By default, cmalign computes the alignment with maximum expected accuracy that is consistent with constraints (bands) derived from an HMM, using a banded version of the Durbin/Holmes optimal accuracy algorithm. cmalign takes special care to correctly align truncated sequences, where some nucleotides from the beginning (5’) and/or end (3’) of the actual full length biological sequence are not present in the input sequence. This behavior is on by default.
For further questions please refere to the Infernal Userguide.