Alignment of Sequences

Using PAM Matrices in Sequence Alignments
David W. Mount
CSH Protocols; 2008; doi:10.1101/pdb.top38 [Abstract] [Full text]

Using BLOSUM in Sequence Alignments
David W. Mount
CSH Protocols; 2008; doi:10.1101/pdb.top39 [Abstract] [Full text]

Using Gaps and Gap Penalties to Optimize Pairwise Sequence Alignments
David W. Mount
CSH Protocols; 2008; doi:10.1101/pdb.top40 [Abstract] [Full text]

A Test of the Markov Model of Evolution in Proteins
David W. Mount
CSH Protocols; 2008; doi:10.1101/pdb.ip58 [Abstract] [Full text]

Comparison of the PAM and BLOSUM Amino Acid Substitution Matrices
David W. Mount
CSH Protocols; 2008; doi:10.1101/pdb.ip59 [Abstract] [Full text]

Studies of Varying Alignment Algorithm, Amino Acid Scoring Matrix, and Gap Penalties
David W. Mount
CSH Protocols; 2008; doi:10.1101/pdb.ip60 [Abstract] [Full text]

Maximum Parsimony Method for Phylogenetic Prediction
David W. Mount
CSH Protocols; 2008; doi:10.1101/pdb.top32 [Abstract] [Full text]

Distance Methods for Phylogenetic Prediction
David W. Mount
CSH Protocols; 2008; doi:10.1101/pdb.top33 [Abstract] [Full text]

The Maximum Likelihood Approach for Phylogenetic Prediction
David W. Mount
CSH Protocols; 2008; doi:10.1101/pdb.top34 [Abstract] [Full text]

Choosing a Method for Phylogenetic Prediction
David W. Mount
CSH Protocols; 2008; doi:10.1101/pdb.ip49 [Abstract] [Full text]