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.
http://www.jalview.org
CINEMA is a Colour INteractive Editor for Multiple Alignments.
http://utopia.cs.manchester.ac.uk/cinema
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.
http://bioweb.pasteur.fr/docs/mview/
A tool to remove sequences (taxa) with many gaps in the post-process of alignments in order to improve the alignment area
http://www.cbs.dtu.dk/services/MaxAlign/
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).
http://bio.dfci.harvard.edu/Tools/sva.html
Multiple Align Show accepts a group of aligned sequences (in FASTA or GDE format) and formats the alignment to your specifications. You can specify the number of residues per line, and the font size and font style. You can also set a consensus level, which specifies the fraction of residues that need to be identical or similar in a column of the alignment for highlighting to be added. Use Multiple Align Show to enhance the output of sequence alignment programs.
http://bio.dfci.harvard.edu/Tools/SMS/multi_align.html
Jemboss is a graphical user interface to EMBOSS.
http://emboss.sourceforge.net/Jemboss/
Analyse Multiply Aligned Sequences - not maintained.
http://barton.ebi.ac.uk/servers/amas_server.html
Pairwise Alignments
This tool produces the alignment of two given sequences using BLAST engine for local alignment.
http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi
Pairwise global and local alignment tool (EMBOSS).
http://www.ebi.ac.uk/emboss/align/index.html
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.
http://www.ebi.ac.uk/~guy/exonerate/
PipMaker computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a ``percent identity plot'', or ``pip'' for short.
http://pipmaker.bx.psu.edu/pipmaker/
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.
http://athena.bioc.uvic.ca/workbench.php?tool=jdotter&db=
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.
http://bioinformatics.abc.hu/tothg/biocomp/other/Dotter.html
Multiple Alignments
CLustalW alignment software online and download versions.
http://www.ebi.ac.uk/Tools/clustalw2/index.html
MAFFT (Multiple Alignment using Fast Fourier Transform) is an online high speed multiple sequence alignment program.
http://www.ebi.ac.uk/mafft/
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.
http://www.ebi.ac.uk/muscle/
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures
http://www.tcoffee.org/
an open graphical environment for sequence analysis
http://gi.cebitec.uni-bielefeld.de/qalign
DNA and protein sequence alignment based on segment-to-segment comparison
http://bioinfo.genopole-toulouse.prd.fr/multalin/multalin.html
DNA and protein sequence alignment based on segment-to-segment comparison
http://bibiserv.techfak.uni-bielefeld.de/dialign/
This service calculates pair-wise and multiple alignments of genomic sequences using CHAOS and DIALIGN
http://dialign.gobics.de/chaos-dialign-submission
An Algorithm for Constrained Alignment of Multiple Data Sequences
http://cbcsrv.watson.ibm.com/Tmsa.html
Multiple Sequence Alignment Using Partial Order Graphs; see also software project on sourceforge: http://sourceforge.net/projects/poamsa/
http://bioinfo.mbi.ucla.edu/poa2/
LALIGN - find multiple matching subsegments in two sequences
http://www.ch.embnet.org/software/LALIGN_form.html
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.
http://bibiserv.techfak.uni-bielefeld.de/dca/submission.html
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.
http://baboon.math.berkeley.edu/mavid/
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.
AliWABA is a website and portal for ABA, the A-Bruijn Aligner for the Multiple Alignment of Sequences with Repeated and Shuffled Elements
http://aba.nbcr.net/
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.
http://bioinfo.lifl.fr/magnolia/index.php
cDNA/RNA/EST-to-Genome Alignments
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.
http://origin.bic.nus.edu.sg/mgalign/index.html
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.
http://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi
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.
http://www.ncbi.nlm.nih.gov/IEB/Research/Ostell/Spidey/
E2G is a web based-tool which efficiently maps large EST and cDNA data sets to genomic DNA. The server hosts huge EST databases of a few GB in size in indexed data structure.
http://bibiserv.techfak.uni-bielefeld.de/e2g/
sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene.
http://pbil.univ-lyon1.fr/sim4.php
Protein-to-Genome Alignements
Nucleotide Amino Acid Alignment (NAP) is a Java interface to the nap C program. The NAP program computes an optimal global alignment of a DNA sequence and a protein sequence without penalizing terminal gaps. NAP handles frameshifts and long introns in the DNA sequence. It delivers the alignment in linear space, so long sequences can be aligned. The experimental results demonstrate that NAP is a sensitive and powerful tool for finding genes by DNA-protein sequence homology.
http://athena.bioc.uvic.ca/workbench.php?tool=nap&db=