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A whole genome pairwise and multiple alignment editor. The program highlights differences between pairs of alignments and allows the user to easily navigate large alignments of similar sequences. Although Base-By-Base was intended as an editor and viewer for alignments of highly similar sequences, it is also provides many of the functions of other generic alignment editors. In addition to visualizing genomes and protein sequences, Base-By-Base allows the user to estimate simple phylogenetic trees, calculate the numbers of conserved and non-conserved sequence positions, and test simple quantitative hypothesis using novel modifications.

BLAT / BLAST-Like Alignment Tool

Finds genomic sequences that match a protein or DNA sequence submitted by the user. BLAT is a very fast sequence alignment tool similar to BLAST typically used for searching similar sequences within the same or closely related species. It was developed to align millions of expressed sequence tags and mouse whole-genome random reads to the human genome at a higher speed. BLAT is commonly used to look up the location of a sequence in the genome or determine the exon structure of an mRNA, but expert users can run large batch jobs and make internal parameter sensitivity changes by installing command line it on Linux server.


Allows user to detect evolutionarily conserved regions (ECRs). zPicture is an automated alignment and visualization tool to generate reliable, highly sensitive single or multiple pairwise sequence alignments. This tool supplies results in a visually compact and interactive manner. It is useful to study large genomic regions of any length from microbes to human. It also can analyze alignments for the presence of conserved transcription factor-binding sites (TFBS) via the rVista tool portal.


Identifies all independent partial and complete copies of genes with similarity to a certain genomic region. BLAST2GENE is capable of interpreting a series of high scoring pairwise alignments (HSPs) from a BLAST comparison of a query sequence (normally protein or cDNA) with a genomic region. The action of the program can be divided into three main steps: (1) parsing the BLAST output; (2) identification and delimitation of genes or gene copies based on the parsed output and (3) generation of graphical output.

Parasail / Pairwise Sequence Alignment Library

Contains implementations of global, semi-global and local pairwise sequence alignment algorithms. Parasail uses a 375 query sequences with a speed of 136 billions cells update per second. It executes this algorithms for vectorized pairwise sequence alignment in order to propose an implementation of the best-performing algorithms. This achievement is done in two ways: (1) returning the alignment score and ending locations, (2) returning alignment statistics.

Spaced Words

A package to alignment-free sequence comparison. Spaced Words uses one or a whole set pattern of care and doesn't care positions: the occurrence of a spaced word in a sequence is then defined by the characters at the match positions only, while the characters at the don't care positions are ignored. It compares the frequencies of the spaced words according to the pre-defined pattern. An information-theoretic distance measure is then used to define pairwise distances on the set of input sequences based on their spaced-word frequencies.

AGA / Advanced Genome Aligner

Helps is align an unknown nucleic acid sequence against a (reference) genome. AGA is a method developed to align any nucleic acid sequence against any genome for which Coding Sequence feature annotations are available. By considering amino acid sequence similarity across all Coding Sequences, this application outstrips the large diversity caused by the high rate of evolution, and deals properly with overlapping reading frames common to these viruses. This application is available as a web application and as command-line application.

GLASS / GLobal Alignment SyStem

Aligns pairs of homologous DNA sequences. GLASS is designed for aligning long, divergent sequences that contain blocks of moderate to strong homology, such as orthologous/paralogous pairs of genes. First, a rough alignment map is constructed by finding long segments that match exactly, and whose flanking regions have high similarity. The procedure is repeated on the intervening regions using successive smaller matching segments. Finally, the remaining short unaligned regions are aligned using standard alignment techniques. A web page provides access to an online GLASS server. If users wish to use GLASS for batch jobs or very large sequences, the stand-alone version can be downloaded.

NemaFootPrinter / Nematode Transcription Factor Scan Through Philogenetic Footprinting

Assists researchers in the identification of conserved non-coding sequence regions between the genomes of the two nematodes C. elegans and C. briggsae. NemaFootPrinter is a web application that proceeds to the identification of conserved functional segments outside exons (putative new gene expression control elements) through comparative genomics. Moreover, the investigator can retrieve the genome DNA sequences of the two orthologous genes, visualize graphically the genes' intron/exon structure and the surrounding DNA regions.

GATA / Graphic Alignment Tool for comparative sequence Analysis

A standalone, platform independent, graphic alignment tool for comparative sequence analysis. GATA uses the NCBI-BLASTN program and extensive post-processing to identify all small sub-alignments above a low cut-off score. These are graphed as two shaded boxes, one for each sequence, connected by a line using the coordinate system of their parent sequence. Shading and colour are used to indicate score and orientation. A variety of options exist for querying, modifying and retrieving conserved sequence elements. Extensive gene annotation can be added to both sequences using a standardized General Feature Format (GFF) file.


Allows users to find multiple alignment from nucleotide sequences. BlastAlign can produce a matrix displaying regions of homology along the sequences. It proceeds first to a selection of the ‘most representative’ sequence, and then extracts blastn query-anchored multiple alignment for this sequence. This allows subgroups to be identified visually, and an option permits users to create new multiple alignments based on user-selected sequences. It includes a perl program, named BlastAlignP, aligning nucleotide sequences to a single amino acid sequence.


Obtains a global alignment between two sequences in quadratic time and space. zAlign is a local sequence aligner, especially intended for use with large biological DNA sequences, with more than 1Mbp. It produces optimal local alignments in four phases (i) the sequences to be compared are sent to all processors, (ii) it calculates the similarity matrix with affine gap in linear space, (iii) it sends the score found, the coordinates and the divergences to processor and (iv) it obtains the best local alignments in limited memory space.


Calculates an optimal global alignment of two sequences using a modification of the classic dynamic programming algorithm which uses linear space. Stretcher is an Emboss tool that uses Needleman-Wunsch method. The output is a standard alignment file. The substitution matrix, gap insertion penalty and gap extension penalties used to calculate the alignment may be specified. This program implements the Myers and Miller algorithm for finding an optimal global alignment in an amount of computer memory that is only proportional to the size of the smaller sequence - O(N).


Reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. needleall uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length. The algorithm uses a dynamic programming method to ensure the alignment is optimum, by exploring all possible alignments and choosing the best. A scoring matrix is read that contains values for every possible residue or nucleotide match. Needleall finds the alignment with the maximum possible score where the score of an alignment is equal to the sum of the matches taken from the scoring matrix, minus penalties arising from opening and extending gaps in the aligned sequences. The substitution matrix and gap opening and extension penalties are user-specified.


Compares two sequences looking for local sequence similarities. LALIGN produces k best “non-intersecting” local alignments for any chosen k. It needs only O(M + N + K) space, where M and N are the lengths of the given sequences and K is the total length of the computed alignments. The tool reports a number of non-overlapping alignments between sequences. LALIGN is a “linear-space algorithm” in the sense that it needs only space proportional to the sum of the input size and the output size.

TIP / Traducción Inversa de Proteínas

Applies genetic algorithms to improve the backtranslation, by minimizing the difference of some coding statistics with respect to their average value in the target. TIP works on sequence files and generates some files in formats of its own, mainly for parameters and species profiles. It currently computes (and imitates) G + C level, relative codon usage, IDH, discrete Fourier transform and autocorrelations functions. It may be useful for understanding the changes in genes after horizontal transfer to a new species, and for creating surrogate data in diverse applications.