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MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is a computer software for multiple sequence alignment of protein and nucleotide sequences. It is licensed as public domain. The method was published by Robert C. Edgar in two papers in 2004. The first paper, published in Nucleic Acids Research, introduced the sequence alignment algorithm ...
Clustal Omega, ClustalW2, MAFFT, MUSCLE, BioJava are integrated to construct alignment Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using Archaeopteryx: Software is package of 7 interactive visual tools for multiple sequence alignments. Major focus is manipulating large alignments.
linked DNA to Protein multiple alignment with MUSCLE, Clustal and Smith-Waterman: Both: Local or global: DNADynamo: 2004 (newest version 2017) EDNA Energy Based Multiple Sequence Alignment for DNA Binding Sites: Nucleotides: Local or global: Salama, RA. et al. 2013: FAMSA Progressive alignment for extremely large protein families (hundreds of ...
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences.
It offers various alignment methods and strategies, including iterative refinement and consistency-based approaches, that further enhance accuracy and robustness of alignments. As a result, MAFFT is widely recognized as a powerful tool for multiple sequence alignment and is highly appreciated by the scientific community. [20]
Progressive multiple sequence alignment: Distance matrix/nearest neighbor: Thompson et al. [13] CoalEvol Simulation of DNA and protein evolution along phylogenetic trees (that can also be simulated with the coalescent) Simulation of multiple sequence alignments of DNA or protein sequences M. Arenas, D. Posada CodABC
Circular Multiple Sequence Alignment where the start and end of protein sequences can vary to find better matches. Circular multiple sequence alignment – A common assumption of multiple sequence alignment techniques is that the left- and right-most positions of the input sequences are relevant to the alignment. However, the position where a ...
M-Coffee: a special mode of T-Coffee that makes it possible to combine the output of the most common multiple sequence alignment packages (Muscle, ClustalW, Mafft, ProbCons, etc.). The resulting alignments are slightly better than the individual one, but most importantly the program indicates the alignment regions where the various packages ...