Alignment
| 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, but OSX version has been unstable. |
| 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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