Multiple sequence alignment (MSA) is a key component in almost every comparative analysis of biological sequences (DNA or proteins). Moreover, MSA reconstruction is often the first step in bioinformatic pipelines, where MSA is later used for further analyses.
Manages and manipulates life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. It is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists. It provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project.
Converts a protein sequence alignment into the corresponding codon alignment. PAL2NAL is a web server allowing users to obtain codon alignments for specific regions of interest, such as functional domains or particular exons by selecting the positions in the input protein sequence alignment. The software can be used to construct codon multiple alignments, which are required in many molecular evolutionary analyses.
Allows users to perform the alignment of multiple related sequences. MultAlin is a platform based on an algorithm exploiting progressive pairwise alignment that considers relationships that can exist among some subsets of sequences. The application includes options to set the desired output format and its size and colors as well as configure personalized alignment parameters such as the number of iterations and the gap penalties required.
Allows DNA, RNA and protein sequence alignment and analysis. DNASTAR Molecular Biology Suite is a sequence analysis and alignment software that provides tools for several molecular biology workflows, including DNA, RNA and protein edition and annotation, Sanger sequence assembly, multiple sequence alignment (MSA), virtual cloning, primer design as well as sequence analysis.
Provides a multiple protein sequence alignment. MUSCLE uses two distance measures for a pair of sequences: a kmer distance (for an unaligned pair) and the Kimura distance (for an aligned pair). This application has three stages: it (i) builds a progressive alignment, (ii) improves the tree and builds a new progressive alignment according to this tree, and (iii) performs iterative refinement using a variant of tree-dependent restricted partitioning.
Provides several tools for sequence database maintenance and analysis. ARB is a graphically oriented package that consists of software tools directly interacting with one another as well as the central database, which are controlled via a common graphical interface. It includes software for visualization, sequence edition, profiles determination, filtering, phylogenetic treeing, sequence alignment, probe design and evaluation and data import and export.