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About Press Copyright Contact us Creators Advertise Developers Terms Privacy Policy & Safety How YouTube works Test new features Press Copyright Contact us Creators. CodonCode Aligner is easy to learn and use, yet powerful and highly customizable. It includes extensive, context-sensitive help with 'how to' instructions and explanations about the algorithms used. CodonCode Aligner is widely used in phylogenetics, evolution research, biogeography, mutation detection, and other biomedical research areas. CodonCode Aligner to clean your sequences and then BioEdit to align multiple sequence. BioEdit also has a built-in CLUSTALW for multiple alignment. Software similar to or like CodonCode Aligner Commercial application for DNA sequence assembly, sequence alignment, and editing on Mac OS X and Windows. Scripting in CodonCode Aligner 2.0.6 by bbimber » Mon Sep 22, 2008 11:58 pm 1 Replies 8279 Views Last post by Peter Richterich Thu Sep 25, 2008 3:22 pm; Printing problems in CodonCode Aligner 2.0.6 by Axa » Tue Sep 23, 2008 10:00 pm 1 Replies 7968 Views Last post by Peter Richterich Thu Sep 25, 2008 3:18 pm.

Commercial application for DNA sequence assembly, sequence alignment, and editing on Mac OS X and Windows.Wikipedia

• Staden Package

  Computer software, a set of tools for DNA sequence assembly, editing, and sequence analysis. Open-source software, released under a BSD 3-clause license.Wikipedia

• DNADynamo

  Commercial DNA sequence analysis software package produced by Blue Tractor Software Ltd that runs on Microsoft Windows, Mac OS X and Linux Used by molecular biologists to analyze DNA and Protein sequences.Wikipedia

• MacVector

  Commercial sequence analysis application for Apple Macintosh computers running Mac OS X. Intended to be used by molecular biologists to help analyze, design, research and document their experiments in the laboratory.Wikipedia

• DNA sequencing theory

  Broad body of work that attempts to lay analytical foundations for determining the order of specific nucleotides in a sequence of DNA, otherwise known as DNA sequencing. The practical aspects revolve around designing and optimizing sequencing projects (known as 'strategic genomics'), predicting project performance, troubleshooting experimental results, characterizing factors such as sequence bias and the effects of software processing algorithms, and comparing various sequencing methods to one another.Wikipedia

• Consed

  Program for viewing, editing, and finishing DNA sequence assemblies. Originally developed for sequence assemblies created with phrap, recent versions also support other sequence assembly programs like Newbler.Wikipedia

• Bowtie (sequence analysis)

  Software package commonly used for sequence alignment and sequence analysis in bioinformatics. Distributed freely and compiled binaries are available for Linux, macOS and Windows platforms.Wikipedia

• Sequence assembly

  In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. Needed as DNA sequencing technology cannot read whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used.Wikipedia

• Newbler

  Software package for de novo DNA sequence assembly. Designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Sciences, a Roche Diagnostics company.Wikipedia

• DNA sequencing

  Process of determining the nucleic acid sequence – the order of nucleotides in DNA. Used to determine the order of the four bases: adenine, guanine, cytosine, and thymine.Wikipedia

• FASTA

  DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. FASTA format which is now ubiquitous in bioinformatics.Wikipedia

• Yass (software)

  Free software, pairwise sequence alignment software for nucleotide sequences, that is, it can search for similarities between DNA or RNA sequences. YASS accepts nucleotide sequences in either plain text or the FASTA format and the output format includes the BLAST tabular output.Wikipedia

• Sim4

  Nucleotide sequence alignment program akin to BLAST but specifically tailored to DNA to cDNA/EST alignment (as opposed to DNA–DNA or protein–protein alignment). Written by Florea et al.Wikipedia

• Phrap

  Widely used program for DNA sequence assembly. Part of the Phred-Phrap-Consed package.Wikipedia

• BLAST (biotechnology)

  Algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query) with a library or database of sequences, and identify database sequences that resemble the query sequence above a certain threshold.Wikipedia

• Tree alignment

  Computational problem concerned with producing multiple sequence alignments, or alignments of three or more sequences of DNA, RNA, or protein. Sequences are arranged into a phylogenetic tree, modeling the evolutionary relationships between species or taxa.Wikipedia

• Alignment-free sequence analysis

  In bioinformatics, alignment-free sequence analysis approaches to molecular sequence and structure data provide alternatives over alignment-based approaches. The emergence and need for the analysis of different types of data generated through biological research has given rise to the field of bioinformatics.Wikipedia

• Sequerome

  Web-based sequence profiling tool for integrating the results of a BLAST sequence-alignment report with external research tools and servers that perform advanced sequence manipulations, and allowing the user to record the steps of such an analysis. Web-based Java tool that acts as a front-end to BLAST queries and provides simplified access to web-distributed resources for protein and nucleic acid analysis.Wikipedia

• Smith–Waterman algorithm

  The Smith–Waterman algorithm performs local sequence alignment; that is, for determining similar regions between two strings of nucleic acid sequences or protein sequences. Instead of looking at the entire sequence, the Smith–Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure.Wikipedia

• List of sequence alignment software

  Compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins.Wikipedia

• Social sequence analysis

  Special application of sequence analysis, a set of methods that were originally designed in bioinformatics to analyze DNA, RNA, and peptide sequences. Social sequence analysis involves the examination of ordered social processes, ranging from microsocial interaction patterns (for example, turn-taking dynamics in conversations) and interpersonal contact dynamics to the development of social hierarchies and macrosocial temporal patterns.Wikipedia

• Phyloscan

  Web service for DNA sequence analysis that is free and open to all users . For locating matches to a user-specified sequence motif for a regulatory binding site, Phyloscan provides a statistically sensitive scan of user-supplied mixed aligned and unaligned DNA sequence data.Wikipedia

• Sequence clustering

  In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences can be either of genomic, 'transcriptomic' (ESTs) or protein origin.Wikipedia

• Stockholm format

  Multiple sequence alignment format used by Pfam and Rfam to disseminate protein and RNA sequence alignments. The alignment editors RaleeWikipedia

• MUMmer

  Bioinformatics software system for sequence alignment. Based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task, enabling it to be applied to very long sequences.Wikipedia

• Sequence logo

  Graphical representation of the sequence conservation of nucleotides or amino acids (in protein sequences). Created from a collection of aligned sequences and depicts the consensus sequence and diversity of the sequences.Wikipedia

• Clustal

  Series of widely used computer programs used in Bioinformatics for multiple sequence alignment. There have been many versions of Clustal over the development of the algorithm that are listed below.Wikipedia

• SAM (file format)

  Text-based format originally for storing biological sequences aligned to a reference sequence developed by Heng Li and Bob Handsaker et al. Widely used for storing data, such as nucleotide sequences, generated by next generation sequencing technologies, and the standard has been broadened to include unmapped sequences.Wikipedia

• Short Oligonucleotide Analysis Package

  Suite of bioinformatics software tools from the BGI Bioinformatics department enabling the assembly, alignment, and analysis of next generation DNA sequencing data. Particularly suited to short read sequencing data.Wikipedia

• Jalview

  Piece of bioinformatics software that is used to look at and edit multiple sequence alignments. Originally written by Michele Clamp whilst working in Geoff Barton's group at the University of Oxford and European Bioinformatics Institute .Wikipedia

Sentences forCodonCode Aligner

• Phred is distributed commercially by CodonCode Corporation, and used to perform the 'Call bases' function in the program CodonCode Aligner.Phred base calling-Wikipedia
• Programs like Sequencher use quality scores for display, end clipping, and consensus determination; other programs like CodonCode Aligner also implement quality-based consensus methods.Phred quality score-Wikipedia
• For users who want to use Phrap from a graphical interface, the commercial programs MacVector (for Mac OS X only) and CodonCode Aligner (for Mac OS X and Microsoft Windows) are available.Phrap-Wikipedia

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