Alignment viewer with BioJS MSA viewer.
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.
Clustal Omega is a general purpose multiple alignment program for DNA or proteins.
GLProbs is an HMM generalisation of MSAprobs and makes use of an adaptive guide tree construction method. It is reported to be even more accurate than MSAProbs. [GLProbs 1.0; http://sourceforge.net/projects/glprobs/]
HHalign compares two alignments with each other by pairwise alignment of HMMs. It shows the optimal alignment and all significant non-overlapping 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 - a fairly accurate and very fast multiple sequence alignment algorithm.
A very accurate multiple alignment program for amino acid or nucleotide sequences. (MAFFT: Multiple sequence Alignment based on Fast Fourier Transform) [MAFFT v7; http://mafft.cbrc.jp/alignment/software/]
One of the most accurate multiple alignment algorithms for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. http://msaprobs.sourceforge.net/homepage.htm#latest
MUSCLE: Multiple Sequence Comparison by Log-Expectation. [MUSCLE v3.8; http://www.drive5.com/muscle/]
ProbCons is a very accurate tool for generating multiple alignments of protein sequences
[ProbCons v1.12; http://probcons.stanford.edu/]
Multiple sequence alignment tool for protein and nucleotide sequences. (T-Coffee:Tree-based Consistency Objective Function for alignment Evaluation). [T-Coffee 11.0; http://www.tcoffee.org/]