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GeneDoc is a full-featured multiple sequence alignment editor, analyzer, and shading utility for Windows. It offers an intuitive graphical interface similar to the one implemented in XiYOS, but it contains an extended set of features, including sequence and alignment viewing and editing, multiple output styles, flexible, interactive alignment editor, simple sequence input, and saving, basic graph plotting. The program allows you to draw the blocks that represent the sequences in the file either from scratch or from a template, and you can also load sequences from various sources. GeneDoc is a tool for the visual analysis and editing of multiple sequence alignments. It has been used to create presentations for posters, talks, and scientific journals.

The main goal of this application is to create and manipulate multiple sequence alignment graphics such as those produced by ClustalW, MAFFT, and other alignment software. It takes a structural format input file, consisting of a multiple sequence alignment and associated tree, and produces a high quality publication-ready image in PNG or GIF format loaded directly into your favorite presentation package or a PostScript file which can be printed on a high-resolution printer. GeneDoc enables scientists to efficiently perform sequence alignment, display and analyze multiple sequences, and evaluate DNA, protein, and amino acid homologies. The software is built on an advanced multiple sequence alignment engine, which allows researchers to trace the evolutionary history of a group of related sequences. The program includes many features that aid in analyzing nucleotide or amino acid alignments and provides maximum flexibility during sequence manipulation.

Geneious is one of the classical platforms that combines all the major DNA and protein sequence analysis tools into one revolutionary software solution. It is an integrated system for handling, processing, displaying, and analyzing all types of gene sequences. It provides a complete solution for manipulating gene sequencing, genomic mapping, and genetic screens. It lets all the tools required to perform the entire pre-annotation workflow, including data import/export, alignment, and annotation.

It includes powerful sequence editing, alignment, and analysis tools, combined with a fast and intuitive graphical user interface that leads the market in functionality. It has been designed from the ground up to take advantage of modern computer hardware, running faster than ever before. Users can enjoy the added advantage of multi-threaded operation for increased speed and responsiveness, as well as support for multiple processors for extra performance.

UGENE is open-source software for DNA and protein sequence visualization, alignment, assembly, and annotation, and it is completely compatible with Bioinformatics methods. It supports popular alignment formats, modern DNA and protein annotation pipelines, as well as a variety of popular file formats like fasta, fastq, fas, phd, EMBL. It includes methods for most common molecular biology tasks: multiple sequence comparison, alignments visualization, sequence assembly, gene finding, and much more UGENE’s graphical interface relies on the Qt framework and provides a simple yet intuitive way for alignment of DNA and RNA sequence fragments.

The sequence is presented as a matrix where columns represent fragments and rows represent positions of fragments in the reference sequence. The fragments can be sorted by quality or by similarity. It incorporates most modern data analysis and interpretation techniques, such as sequence alignment and assembly, gene expression analysis, phylogenetic tree and network reconstructions, modeling of regulatory sites, protein engineering, and many others.

Genophore is one of the interesting applications for searching and designing proteins. It provides a suite of bioinformatics utilities. It can be used for protein structure prediction, finding protein domains, or any other sequence or feature annotation. It requires some protein sequence to execute its search but can also accept input from a number of file formats, such as PDB and SWISS-PROT, and does not produce any results that are not found in the GenBank database.

Genophore takes a novel approach to protein design by using sequence-based bioinformatics tools to pick a suitable sequence of amino acids, in much the same way that you might use a spell checker to make a typo-free copy. It can be used to pick a sequence of acids consistent with some known properties, e.g., a green fluorescent protein whose emission wavelength is visible to the human eye, or it can be used to perform a search: imagine you have your own sequence of acids, and you want to find the proteins those acids might code for, in order to make some rational design choices. Paid sass

Clustal X is one of the widely used computer programs used in bioinformatics for multiple sequence alignment. As such, it can be used to carry out complete genome sequencing. It uses the method of progressive alignment, which optimizes the alignments with a slowing down series of suboptimal heuristic methods until all possible pairs fall within an acceptable distance of each other. It works by the progressive alignment of sequences. In progressive alignment, the most similar regions are aligned first, and subsequent rounds of alignment explore the alignments of shorter and shorter regions until the whole sequence has been aligned.

It is distributed by a number of major sequencing centers as well as being available to individuals via anonymous ftp at many locations worldwide. Clustal is widely used for multiple global alignments of protein sequences, either within species or across distantly related species. Its primary purpose is to identify regions of conservation across the alignment and to generate phylogenetic trees based on sequence similarity. The software can also generate multiple alignments in FASTA format and can be used as a web server.

CLC Main Workbench is one of the cost-effective analysis packages for advanced DNA, RNA, and protein analyses. The main workbench offers a common user interface and consistent data structures for a seamless experience across all applications. It provides a complete range of modern tools for the exploration of genetic data and offers a clear and intuitive user interface to enable the efficient exploration of large amounts of data. It supports upstream and downstream processing, including visualization, annotation, filtering, statistics, analysis of variability, and analysis of genome copy number aberrations. Advanced import and export facilities offer flexible data management systems and enable data exchange with other programs.

Furthermore, It is linked to the CLC Sequence Viewer and CLC BioImage Workbench and therefore allows visual inspection of the data. The package contains various tools for the analysis of molecular biology data, implemented in Java and C/C++. The easy-to-use, platform-independent, and open-source software package is designed for academic, industrial, and clinical research facilities. Some of the key features are the support of massive data sets, standardized operating procedures, advanced memory management, and many others. The following modules are available: SeqMan NGS, SeqMan Pro, FASTA, MUSCLE, MUMmer, Bowtie, SOAPaligner/SOAPdenovo, and many more.

TreeView is one of the classical programs for displaying and printing phylogenies. It covers trees often called cladograms which show the evolutionary relationships among groups of organisms; they are often displayed using a program called a phylogenetic tree viewer. It is a program for displaying and printing phylogenies. It can be run in an ordinary terminal window or under X-Windows, and it can draw a tree in one of several standard formats. Its output can be a PostScript file that can be printed on any PostScript printer or, better yet, a compressed file that can be sent by electronic mail to people who have no program or printer that can handle PostScript.

One of the features of TreeView is that it can draw trees using any suitable program for inferring trees from data. In most cases, all you have to do is provide TreeView with the name of the inference program and the name of a file containing your data. It has been written for use with the general public in mind so that you don’t need to be an expert in producing phylogenies. TreeView can create many different trees, including cladograms, phylograms, neighbor-joining trees, and more. You can show your tree as a list, with branches labeled by length, or you can display it in a matrix or as a strict consensus tree.

FigTree is one of the efficient programs that is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. It can be used to quickly create figures for inclusion in publications or to make glossy figures that you can use for presentations. It has been introduced with ease-of-use in mind so that you can get results quickly, but it also has many advanced features if you wish to harness them.

FigTree is developed to be a graphics viewer like Image, Adobe Illustrator, or Inkscape for viewing phylogenetic trees and producing publication-ready figures. It is implemented in Java, which means it can run on multiple platforms, and it has an extensive set of features for manipulating DNA sequences, sequences alignment data, trees, and associated annotation. The algorithmic core of FigTree has been written from scratch to achieve a performance level comparable with dedicated tree-drawing programs. However, it also includes many features from other tree viewers, such as coloring by taxon or annotation attributes. In addition, it saves data in the DOT language for input to other phylogenetic programs.

BioEdit is an open-source software tool that allows biological sequence alignment and editing. It is an easy-to-use tool that provides seamless integration of an alignment viewer with an intuitive GUI. However, it has since been modified to work with protein and translated nucleotide sequences as well. The software may be used to manipulate DNA, RNA, and protein sequences, to produce nucleotide and translated protein alignments in a variety of formats, and to edit DNA, RNA, or protein sequence alignments.

This enables users to carry out a number of different tasks, including production of informative dot-plots of pairs of aligned nucleotide or translated protein sequences; production of informative sequence logos describing a number of aligned nucleotides or translated protein sequences; production of multiple sequence alignments; testing the statistical significance of matches between two sets of sequences by producing position-specific score matrices and carrying out bootstrap analyses to determine the confidence limits on those scores; production of consensus sequence alignments from a number of input sequences that contain non-consensus regions; editing an existing alignment. BioEdit is designed to handle not only basic sequence alignment and difference analysis applications but also the manipulation of multiple sequences and annotation of those sequences. The software is modular, allowing the user to assemble a customized set of tools for sequence manipulation.

RasMol is one of the classical molecular graphics programs intended for the visualization of proteins, nucleic acids, and small molecules. It can show you a range of different types of 3D or 2D representations of your data rings, sticks, space-filling, surfaces, and many more. It uses a combination of 3D solid and surface rendering and has an extensive collection of built-in molecular objects. The visualization can be further supplemented by molecular dynamics using either the GROMOS or CHARMM force fields, and additional objects may be added using the OBJ format.

The core consists of a fast and intuitive hierarchical display system that is user-configurable by means of “drag and drop” software tools. The display system can accommodate multiple sequences or sequence ranges and can be used as an output device for simple sequence analysis functions. Full editing functions are supported for DNA, RNA, and protein sequences. The following information is maintained for each sequence: name, author, sequence comments, sequence identifier accession number, UniGene ID number or a custom user-defined number, source organism, date created/edited, date last modified, and date last saved.

Clustal Omega is a rich-featured multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. The program can be used for tree construction. The statistical significance of the alignment is assessed by resampling the input data with a bootstrap algorithm combined with other distance measures. The alignments can be viewed as a conservative consensus or as equal-cost multipath alignments. Clustal Omega is the most powerful and fastest alignment program ever developed.

It is based on the highly successful Clustal W program and has many new features like automated construction of guide trees based on DNA and protein sequence data, or HMM-profiles, automated profile-profile alignments, use of user-provided sequences for modeling unknown sequences, a robust measure of pairwise homology based on the similarity between HMM-profiles and many others. An alignment can then be constructed by translating the seed alignment profile along the sequence to produce a set of consensus-like alignment positions. As well as offering improvements on speed and accuracy over previous methods, this approach enables greater sensitivity to conserved regions within longer sequences and improves the ability to deal with divergent or distantly related sequences.

SnapGene Viewer is one of the revolutionary software that allows molecular biologists to create, browse, and share richly annotated DNA sequence data. It is a desktop tool for viewing, editing, and annotating DNA sequence files such as FASTA and XML. Annotated data can then be exported as a variety of formats such as PDFs, image files, or searchable genome browser databases such as UCSC Genome Browser. Users can open their DNA sequence files on their computers and display them with a range of different views. It stands out from other molecular biology software because it uses both data and software from third-party providers.

This gives an ability to display not only DNA sequence but also more advanced data such as chromatograms, motifs, gene expression levels, and protein structure data. With you can import and organize your DNA sequencers files. You can then search this database of DNA sequences and focus on the ones most likely to contain your gene of interest. The program will then go through the database and identify matches to the DNA segments in your query. SnapGene Viewer makes it possible to quickly examine where a gene of interest is located within a DNA sequence, why it is there in this specific location, what other genes are encoded there, and much more.

Vector NTI software is a completely integrated suite of sequence analysis and design tools that help you manage, view, analyze, transform, share, and document your genomic data. It includes tools that are used in clinical laboratories and research laboratories around the world to create DNA sequencing and mapping data, accesses publicly available sequence data from UCSC Genome Browser, and more; compile sequence and annotation data from numerous sources into a single easy-to-manage database; create analysis sequences to search for desired targets; predict the function of open reading frames; design primers for PCR or FISH application; and simply share your information including a GenBank submission in just a few clicks.

It is a software suite for the manipulation, analysis, publication, and presentation of all types of biological sequences and data. It includes a collection of companion products for sequence assembly, variant analysis, data visualization, and basic graphics. It makes it easy to start from raw files or from databases containing thousands of sequences and to visualize the most complex sets of data in dynamic graphical views. Search for similarities between sequences using motifs or patterns. You can also use vector NTI software to perform analyses such as pairwise or multiple alignments or to extend your DNA sequences with custom-designed primers or restriction sites.

DNADynamo is a commercial DNA sequence analysis software package written in Java. It can be used for basic tasks such as nucleotide comparison and for more advanced tasks such as generating genotype likelihoods. It provides high-performance sequence analysis algorithms implemented entirely in Java. It has a user-friendly GUI for data entry, analysis, and visualization, which uses the Swing toolkit.

The algorithms are highly customizable with parameter settings that allow the bio information to choose between speed, accuracy, or best possible output. It can open the most common file types, including; BAM files, SAM files, genbank format, raw FASTQ format files, trace data in standard ASCII format, and Genome Analyzer II (GAII) binary output files, and also supports the new FAST5 file format.

Ridom TraceEdi is one of the efficient cross-platform graphical DNA trace viewers and editors. The user can quickly navigate through long traces, perform various operations on them, e.g., extract sub-traces, perform basic analysis, etc., and save the results as bitmap image files or text to be further processed by another program. It can read DNAscapes Trace files, which are by default compressed in the DNAscapes rdd format. It also supports the correct reading of files in the compressed zdd format.

The application also offers a rich set of import filters for popular file formats such as FastA, FastN, and Phylip. It is designed for researchers and students, is to provide a graphical editing interface for the commonly used FASTA format DNA sequencing traces. It provides a unique environment that allows researchers to accurately view, print, and interact with all the information associated with a DNA sequence, including chromatograms, sequence traces, markers, analysis results, and sequence annotations.