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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 ...
This page is a subsection of the list of sequence alignment software. Multiple alignment visualization tools typically serve four purposes: Aid general understanding of large-scale DNA or protein alignments; Visualize alignments for figures and publication; Manually edit and curate automatically generated alignments; Analysis in depth
Fast statistical alignment or FSA is a multiple sequence alignment program for aligning many proteins, RNAs, or long genomic DNA sequences. Along with MUSCLE and MAFFT, FSA is one of the few sequence alignment programs which can align datasets of hundreds or thousands of sequences. FSA uses a different optimization criterion which allows it to ...
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.
In bioinformatics, MAFFT (multiple alignment using fast Fourier transform) is a program used to create multiple sequence alignments of amino acid or nucleotide sequences. Published in 2002, the first version used an algorithm based on progressive alignment , in which the sequences were clustered with the help of the fast Fourier transform . [ 2 ]
T-Coffee (Tree-based Consistency Objective Function for Alignment Evaluation) is a multiple sequence alignment software using a progressive approach. [1] It generates a library of pairwise alignments to guide the multiple sequence alignment.
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 ...
A profile HMM modelling a multiple sequence alignment. HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. [2] Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments.