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Servers & Software for Generating Alignments

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  Servers & Software for Generating Alignments
2nd Window Opens resource in a 2nd browser window.

2nd Window ALIGN
[GeneStream] A global alignment of two nucleic acid sequences with no short-cuts.
[more info][10381]

2nd Window ALION
[Stanford Univ.] A multiple sequence alignment tool.
[more info][10345]

2nd Window AMAS: Analyze Multiple Alignments of Protein Sequences
[EBI] Allows the identification of functional residues by comparison of sub-groups of sequences arranged on a tree.
[more info][11235]

2nd Window AMPS
[EBI] A suite of programs for multiple protein sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures, and also implements flexible pattern matching and database scanning options.
[more info][11148]

2nd Window BCM Search Launcher: Multiple Sequence Alignments
[Baylor College of Medicine] A single page offering services for several multiple alignment methods.
[more info][12157]

2nd Window Bioinformatics & Pattern Discovery
[IBM] Information and bioinformatics related servers developed at IBM. Services include sequence pattern analysis, gene expression analysis, and multiple sequence alignment. Servers may be used online, or the code may be downloaded.
[more info][12148]

2nd Window Block Maker
[Fred Hutchinson Cancer Research Center] "Block Maker finds conserved blocks in a group of two or more unaligned protein sequences, which are assumed to be related, using two different algorithms. At least two protein sequences must be provided to make blocks."
[more info][12159]

2nd Window Clustal W
[Baylor College of Medicine] A multiple sequence alignment program for DNA and protein sequence parameters.
[more info][10354]

2nd Window Clustal W
[GenomeNet] A general purpose multiple alignment program for DNA or proteins.
[more info][10355]

2nd Window Clustal W
[Univ. of Washington] A general purpose multiple alignment program for DNA or proteins.
[more info][10356]

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2nd Window CLUSTAL W
[SGI] This is a multiple sequence alignment program for biological sequences.
[more info][11153]

2nd Window ClustalW
[EBI] ClustalW is a popular and improved multiple alignment program for DNA or proteins.
[more info][11242]

2nd Window DIALIGN
[GSF] DIALIGN is a novel program for multiple alignment. It constructs pairwise and multiple alignments by comparing whole segments of the sequences. No gap penalty is used. This approach is especially efficient where sequences are not globally related but share only local similarities, as is the case with genomic DNA and with many protein families.
[more info][11247]

2nd Window Fast Local Alignment for Gigabases
The Fast Local Alignment for Gigabases site offers Cluster FLAG, a sequence database searching tool based on local alignment of nucleotide sequences, and Pairwise FLAG to perform local alignment between two DNA sequences, especially powerful for genome-genome comparison.
[more info][13772]

2nd Window ITERALIGNv1.1
[Stanford University] (Luciano Brocchieri) A program for the multiple alignment of protein sequences.
[more info][12166]

2nd Window LAMA: Local Alignment of Multiple Alignments
[Fred Hutchinson Cancer Research Center] This program compares multiple protein sequence alignments with each other. The program can search databases of such multiple alignments. The search is for sequence similarities between conserved regions of protein families.
[more info][10455]

2nd Window MASIA
[Sealy Center for Structural Biology] MASIA (Multiple Aligned Sequences Investigation and Analysis) is a program with GUI to search for consistent patterns in multiple aligned sequences. Predictions of secondary structures and inside/outside properties of residues at each position in an aligned sequences are based on generalized rules for globular proteins, which are derived from observations of known 3D-structures of proteins.
[more info][12238]

2nd Window Match-Box
[University of Namur] "The Match-Box software proposes protein sequence alignment tools based on strict statistical criteria. The Match-Box program is particularly suitable for finding and aligning conserved structural motives, in particular in protein core."
[more info][12160]

2nd Window MPSA
[NPSA] "Multiple Protein Sequence Analysis is a stand-alone software package for protein sequence analysis with a high integration level and Web client/server capabilities. It provides many methods and tools, which are integrated into an interactive graphical user interface."
[more info][11263]

2nd Window MSA
[Rice Univ.] A program to do multiple sequence alignment under the sum-of-parts criterion.
[more info][11170]

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2nd Window MSA: Multiple Sequence Alignment
[Washington Univ.] Reads a file containing several protein sequences and attempts to produce a multiple alignment of these sequences, which it will write to standard output. MSA uses the algorithm of Altshcul et al., Gupta et al. or ClustalW.
[more info][10458]

2nd Window MultAlin
[INRA] "Multalin creates a multiple sequence alignment from a group of related sequences using progressive pairwise alignments."
[more info][12162]

2nd Window MView
[National Institute for Medical Research] Converts the results of BLAST, FASTA, and other sequence database searches to a coloured multiple alignment of hits stacked against the query.
[more info][12135]

2nd Window Network Protein Sequence @nalysis
[Institute of Biology and Chemistry of Proteins] [email protected] is an interactive Web server dedicated to protein sequence analysis. Analyses offered include sequence similarity, site detection, multiple alignment, secondary structure prediction, and primary structure analysis. Analyses can be combined in a pipeline. The ANTHEPROT windows program is also available here.
[more info][12376]

2nd Window PhyloBLAST
[Pathogenomics Project, Univ. British Columbia] Do molecular phylogenetics analysis of a protein sequence. Enter the sequence at the site. PhyloBLAST uses BLASTP to find related amino acid sequences in the Swiss-Prot database. Select those sequences desired, for a full phylogenetic analysis, satrting with a ClustalW multiple sequence alignment. A choice of Phylip programs, including parsimony, UPGMA, neighbor joining and distance matrix methods, produces a phylogenetic tree.
[more info][13729]

2nd Window PROBE ftp Site
[NCBI] PROBE is a tool for extraction of multiple alignments from a sequence database.
[more info][12165]

2nd Window SAGA
[Centre National de la Recherche Scientifique] Sequence Alignment by Genetic Algorithm. SAGA is optimally designed for the alignment of less than 20 sequences and less than 400 residues.
[more info][12164]

2nd Window Secondary Structure Alignment Server
[Rutgers] The secondary structure alignment server is an interactive tool that allows sequence alignments to be performed based on iterative combinations of amino acid and secondary structure sequence information.
[more info][13579]

2nd Window Sequence Alignment Utility
[MIPS] Performs pairwise alignments for PROTEIN or DNA sequences.
[more info][10420]


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