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
pam). Visualize sequence similarities with
Multiple sequence alignment — Functions for multiple
sequence alignment (
profalign) and functions that support multiple sequences (
fastaread). 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