Alignment Tools
AlignmentViewer
Alignment viewer with jalview applet.
Blammer
Blammer is a tool to convert BLAST or PSIBLAST output files into multiple alignments. Although BLAST can output the HSP's in multiple alignment format the resulting alignments are frequently excessively gapped. Blammer remedies this by realigning gapped regions using a global multiple alignment program.
ClustalW
ClustalW is a general purpose multiple alignment program for DNA or proteins.
HHalign
HHalign compares two alignments with each other by pairwise alignment of HMMs. It shows the optimal alignment and all significant non-overlappiung suboptimal alignments. It also generates a dotplot for which the profile-profile column score is averaged over a window of variable size. If only one alignment is entered, this is compared to itself. Used in this way, HHalign is a very sensitive repeat-identification tool.
Kalign
Kalign - an accurate and fast multiple sequence alignment algorithm.
MAFFT
Multiple alignment program for amino acid or nucleotide sequences
[MAFFT v5.7; http://align.bmr.kyushu-u.ac.jp/mafft/software/]
MUSCLE
MUSCLE is a multiple alignment program for protein sequences. MUSCLE stands for multiple sequence comparison by log-expectation. [MUSCLE v3.51; http://www.drive5.com/muscle/]
ProbCons
ProbCons is a novel tool for generating multiple alignments of protein sequences
[ProbCons v1.10; http://probcons.stanford.edu/]
TCoffee
T-Coffee (Tree-based Consistency Objective Function for alignment Evaluation)
is one of the most accurate multiple sequence alignment methods for protein and nucleotide sequences.
[T-Coffee v4.45; http://igs-server.cnrs-mrs.fr/Tcoffee/]