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Sequence Alignments
Alignment Editors & Analysis
Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor.
CINEMA is a Colour INteractive Editor for Multiple Alignments.
A tool to remove sequences (taxa) with many gaps in the post-process of alignments in order to improve the alignment area
Jemboss is a graphical user interface to EMBOSS.
SeaView is a graphical multiple sequence alignment editor developped by Manolo Gouy. SeaView is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW/MUSCLE programs to locally improve the alignment.
A Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows.
MView is a tool for converting the results of a sequence database search (BLAST, FASTA, etc.) into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment (MSF, PIR, CLUSTAL, etc.) can be processed. In either case, the output is simply HTML, so the result is platform independent and does not require a separate application or applet to be loaded.
This server calculates the variability in each column of a multiple sequence alignment using the Shannon entropy (H) function. H values range from 0 (only one residue in present at that position) to 4.3 (all 20 residues are equally represented in that position).
LalnView is a graphical program for visualizing local alignments between two sequences (protein or nucleic acids). Sequences are represented by colored rectangles to give an overall picture of the similarities between the two sequences. Blocks of similarity between the two sequences are colored according to the degree of identity between segments.
A visualization environment for comparisons of multiple nucleotide sequence alignment tools
Alignment Colourers
Online server, but you'll need an aligment file MSF or ALN).
The CorreLogo server generates for a given RNA or DNA sequence alignment a three-dimensional representation in VRML format and JavaView JVX format.
Pairwise Alignments
COBALT computes a multiple protein sequence alignment using conserved domain and local sequence similarity information.
Pairwise Sequence Alignment is used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).
SIM is a program which finds a user-defined number of best non-intersecting alignments between two nucleic acid sequences or within a sequence.
Smith-Waterman local alignment.
Align Sequences Nucleotide BLAST.
ACT is a free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation.
Exonerate is a generic tool for pairwise sequence comparison. It allows to align sequences using many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
Jaligner is an open source Java implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment using the affine gap penalty model.
Align sequences with either GAP, SIM, LAN, GAP2, or GAP2.
Dot plot Alignments
Java Dot Plot Alignments (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots.
Dotter is a Linux graphical dotplot program for detailed comparison of two sequences. Here, every residue in one sequence is compared to every residue in the other sequence. The first sequence runs along the x-axis and the second sequence along the y-axis. In regions where the two sequences are similar to each other, a row of high scores will run diagonally across the dot matrix.
Multiple Alignments
COBALT computes a multiple protein sequence alignment using conserved domain and local sequence similarity information.
ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
Clustal: Multiple Sequence Alignment of of nucleic acid and protein sequences.
A fast and accurate multiple sequence alignment algorithm.
MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation. MUSCLE is claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options. The application can be dowloaded.
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures
T-Coffee is a multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methods.
MAFFT (Multiple Alignment using Fast Fourier Transform) is an online high speed multiple sequence alignment program.
an open graphical environment for sequence analysis
DIALIGN is a software program for multiple sequence alignment developed by Burkhard Morgenstern et al. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences
DIALIGN-TX is a substantial improvement of DIALIGN-T that combines greedy and progressive alignment strategies.
MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.
This service calculates pair-wise and multiple alignments of genomic sequences using CHAOS and DIALIGN
LALIGN - find multiple matching subsegments in two sequences
An Algorithm for Constrained Alignment of Multiple Data Sequences
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops
Divide-and-Conquer Multiple Sequence Alignment (DCA) is a program for producing fast, high quality simultaneous multiple sequence alignments of amino acid, RNA, or DNA sequences. The program is based on the DCA algorithm, a heuristic approach to sum-of-pairs (SP) optimal alignment that has been developed at the FSPM over the years 1995-97.
The Lagan Tookit is a set of alignment programs for comparative genomics. The three main components are a pairwise aligner (LAGAN), a multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN). All three are based on the CHAOS local alignment tool and combine speed (regions up to several megabases can be aligned in minutes) with high accuracy.
BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP. An intuitive multiple document interface with convenient features makes alignment and manipulation of sequences relatively easy on your desktop computer.
Align and compare from 2 to 100 sequences online using VISTA.
Visualization and Comparison of consensus Sequences
Align-m is an accurate and highly versatile multiple alignment program.
Magnolia is an advanced multiple alignment program suite for nucleic sequences. It is especially designed for protein-coding RNA sequences or non-coding RNA sequences.
Multiple sequence alignment with hierarchical clustering
PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It's based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events.
MAVID is a multiple alignment program that is suitable for alignments of large numbers of DNA sequences. The sequences can be small mitochondrial genomes or large genomic regions up to megabases long. The MAVID server integrates MAVID with various phylogenetic tree construction programs and visualization tools to allow biomedical researchers who have a collection of related genomic sequences to rapidly identify conserved regions for further analysis.
RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment.
cDNA/RNA/EST-to-Genome Alignments
Spidey is an mRNA-to-genomic alignment program. Spidey - aligns one or more mRNA sequences to a single genomic sequence. Spidey will try to determine the exon/intron structure, returning one or more models of the genomic structure, including the genomic/mRNA alignments for each exon.
Splign - is a utility for computing cDNA-to-Genomic alignments based on a variation of the Needleman-Wunsch algorithm combined with Blast for compartment detection and greater performance. Splign is accurate in determining splice sites and tolerant to sequencing errors.
sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene.
MGAlign (short for mRNA to Genome Alignments) is a program written to quickly and accurately align mRNA sequences to genomic sequences on a personal computer.
The Web Bench
The Web Bench
is the essential companion to the biologist, bringing informational resources and a collection of tools & calculators to facilitate work at the bench and analysis of biological data.
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Sequence Analysis with GenBeans
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