You can select from a list of analysis methods to compare nucleotide or amino acid sequences using pairwise or multiple sequence alignment functions.
Pairwise sequence alignment —
Efficient implementations of standard algorithms such as the Needleman-Wunsch
(nwalign) and Smith-Waterman
(swalign) algorithms for pairwise
sequence alignment. The toolbox also includes standard scoring matrices
such as the PAM and BLOSUM families of matrices (blosum, dayhoff, gonnet, nuc44, pam). Visualize sequence similarities
with seqdotplot and sequence
alignment results with showalignment.
Multiple sequence alignment —
Functions for multiple sequence alignment (multialign, profalign) and functions that support
multiple sequences (multialignread, fastaread, showalignment).
There is also a graphical interface (seqalignviewer)
for viewing the results of a multiple sequence alignment and manually
making adjustment.
Multiple sequence profiles —
Implementations for multiple alignment and profile hidden Markov model
algorithms (gethmmprof, gethmmalignment, gethmmtree, pfamhmmread, hmmprofalign, hmmprofestimate, hmmprofgenerate, hmmprofmerge, hmmprofstruct, showhmmprof).
Biological codes — Look
up the letters or numeric equivalents for commonly used biological
codes (aminolookup, baselookup, geneticcode, revgeneticcode).