alistat is part of the HMMer package. HMMER is an implementation of profile hidden Markov models (profile HMMs) for biological sequence analysis. Profile HMMs are statistical models of multiple sequence alignments. They capture position-specific information about how conserved each column of the alignment is, and which residues are likely.

alistat reports basic statistics about a multiple alignment including the format, the number of sequences, the total number of residues, the average and range of the sequence lengths, the alignment length (e.g. including gap characters) and some percent identities. Input formats accepted include selex, msf and aln.

Sample data on Bio-Liniux for the HMMER package can be found in /usr/software/sampledata/hmmer_demo_data

References:
Krogh, A., Brown, M., Mian, I. S., Sjolander, K., and Haussler, D. (1994). Hidden Markov models in computational biology: Applications to protein modeling. J. Mol. Biol., 235:1501 1531.[Entrez]

Durbin, R., Eddy, S. R., Krogh, A., and Mitchison, G. J. (1998). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge UK.

Eddy, S. R. (1998). Profile hidden Markov models. Bioinformatics, 14:755 763.[Entrez]