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Software OS Webserver Comments
BAli-Phy all No Implements a joint Bayesian estimation of alignment and phylogeny. Instead of inferring trees based on a single fixed alignment, it considers near-optimal alignments when estimating the phylogeny. In addition, it can produce alignments colored to indicate uncertain areas of the alignment. Command-line interface.
BlastAlign all No Uses BLAST to align problematic nucleotide sequences.
Clustal all Yes A classic with many Web servers to be searched online.
FSA *nix Yes A probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Uses machine-learning techniques to estimate gap and substitution parameters on the fly. Can align 100s-1000s sequences using a randomized inference algorithm to reduce the computational cost of MSA, as well as very long sequences using the "anchor annealing" technique.
GRAPe *nix No Uses the Marginalized Posterior Decoding algorithm which uses the posterior distribution of alignments to optimize the correct assignment of homology of individual nucleotides, instead of finding a single most probable alignment. Simulations show that the MPD algorithm has higher sensitivity and specificity than the Viterbi and Needleman-Wunsch algorithms.
JalView all No Alignment viewer. Connects to a webserver to align with T-Coffee or MUSCLE. Visualizes alignment in PCA.
LAGAN all Yes Local & global alignments. To run it locally you must download the source code and compile it. It uses anchoring schemes and VISTA visualization.
MAFFT all Yes Multiple alignment method with high accuracy and speed. Superb!
MAVID all Yes Constrained ancestral alignment of multiple sequences. It is able to effectively align divergent sequences, as well as incomplete unfinished sequences.
MUSCLE all Berkeley & NL & EBI Creates multiple alignments of amino acid or nucleotide sequences. Gets better average accuracy and better speed than CLUSTALW or T‑Coffee.
PipMaker all Yes Graphs the alignment results as per-cent identity plots.
POY all No Simultaneously estimates phylogeny and alignments via Direct Optimization. New version is faster.
ProAlign all No Uses HMMs for probabilistic multiple alignment of nucleotide and amino-acid sequences by a stepwise progressive method.
Probalign all Yes Multiple sequence alignment using partition function posterior probabilities. Both AA and DNA/RNA.
StatAlign all No For Bayesian analysis of protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results.
Squint all No An advanced alignment tool bringing together algorithmic alignment of molecular sequences, with human editing. Parts of the sequences can be realigned. Squint can align a nucleotide sequence by amino acid or codon.
T-Coffee all SIB & EBI More accurate than ClustalW for sequences with less than 30% identity, but slower.
FaBox all Yes An online toolbox for FASTA sequences.
ReadSeq all Yes All-time classic biosequence conversion tool.
Format Converter all Yes Automatic sequence conversion tool.

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