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Tree+multi-alignment; probabilistic-Bayesian; joint estimation: Both + Codons: Global: BD Redelings and MA Suchard: 2005 (latest version 2018) Free, GPL: Base-By-Base Java-based multiple sequence alignment editor with integrated analysis tools: Both: Local or global: R. Brodie et al. 2004: Proprietary, freeware, must register CHAOS, DIALIGN ...
MAFFT is widely considered to be one of the most accurate and versatile tools for multiple sequence alignment in bioinformatics. In fact, studies have shown that MAFFT performs exceptionally well when compared to other popular algorithms such as Clustal W and T-Coffee , particularly for larger datasets and sequences with high degrees 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
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.
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.
MAVID is a multiple sequence alignment program suitable for the alignment of large numbers of DNA sequences. [1] [2] The sequences can be small mitochondrial genomes or large genomic regions up to megabases long. The latest version is 2.0.4.
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YASS (Yet Another Similarity Searcher) [1] [2] is a free software, [3] pairwise sequence alignment software for nucleotide sequences, that is, it can search for similarities between DNA or RNA sequences. YASS accepts nucleotide sequences in either plain text or the FASTA format and the output format includes the BLAST tabular output.