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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
manual alignment ; some software assistance: Nucleotides: Local: J. Blandy and K. Fogel: 1994 (latest version 2007) Free, GPL2 ALLALIGN For DNA, RNA and protein molecules up to 32MB, aligns all sequences of size K or greater, MSA or within a single molecule. Similar alignments are grouped together for analysis. Automatic repetitive sequence ...
This application performs multiple and pairwise sequence alignments, provides alignment editing, and generates phylogenetic trees. Maximum Likelihood (RAxML) and Neighbor-Joining DNASTAR: Mesquite Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
List of proprietary bioinformatics software; List of open-source bioinformatics software; Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: Sequence analysis software. List of sequence alignment software; List of alignment visualization software; Alignment-free sequence analysis
Component-based data mining and machine learning software suite written in C++, featuring a visual programming front-end for exploratory data analysis and interactive visualization, and Python bindings and libraries for scripting
Popular tools for sequence alignment include: Pair-wise alignment - BLAST, Dot plots; Multiple alignment - ClustalW, PROBCONS, MUSCLE, MAFFT, and T-Coffee. A common use for pairwise sequence alignment is to take a sequence of interest and compare it to all known sequences in a database to identify homologous sequences. In general, the matches ...
UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. [1]
Purposes of Alignment Visualization: Aid general understanding of large-scale DNA or protein alignments. When analyzing data, it is helpful to visualize it somehow, to be able to easily spot clear patters or relations. Visualize alignments for figures and publication. It summarizes the multiple sequence alignment in an easy-to-digest form.