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windows default iconCodonCode Aligner Publisher's description

Fast, powerful & affordable sequence asembly, alignment, and mutation detection

CodonCode Aligner is a leading software program for DNA sequence analysis.

Widely used in evolution research, biogeography, and other biomedical fields, it offers many features not found in competing programs, including the ability to compare contigs with ClustalW and muscle, trace sharpening, roundtrip editing, and base calling with PHRED, as well as standard features like assembly, trace and contig editing, end clipping, and mutation detection.

Here are some key features of "CodonCode Aligner":

Import and Export:
В· Import sequence chromatograms in ABI, AB1, or SCF format ; import text files in FASTA, GenBank, or EMBL format
В· Create new text sequences and import from GenBank by accession number
В· Export sequences, consensus sequences, alignments, protein translations to SCF, FASTA, NEXUS/PAUP or Phylip

Sequence Editing and Trimming:
В· Manual editing of sequences and contigs, including delete to sample or contig end and contig splitting
В· Automated editing tools: call or remove ambiguities, match consensus, convert low quality bases to N, undo auto-edits
В· Fast navigation with toolbar buttons or keyboard shortcuts; user-definable regions of interest
В· End clip to remove low quality sequence; remove vector contamination

Sequence Assembly:
В· Assemble fragments using local, end-to-end, or large gap (cDNA to genomic) algorithms
В· Accurate, quality base consensus sequences minimize the need for manual editing
В· Assembly by name to build separate contigs for many clones or specimen
В· Assemble with Phrap

Sequence Alignment:
В· Align to reference sequences; align cDNA to genomic DNA
В· Build "contigs of contigs": align contigs to each other with MUSCLE or Clustal
В· Go back from the contig alignment to the original traces with a double-click
В· Edit the sequence traces, the contig view, or the alignment of contigs, while keeping your data consistency

Restriction Mapping:
В· Build restriction maps using any combination of restriction enzymes
В· Select by size of recognition site, overhang, cut frequency, of manufacturer
В· View as single-line or multi-line maps or as text
В· Select restriction fragments by clicks on restriction maps for copying

Mutation Detection and Analysis:
В· Call secondary peaks in sequence traces
В· Sensitive detection of heterozygous SNPs in assembled or aligned contigs
В· View and export amino-acid level effects of mutations
В· Accurate and sensitive detection of heterozygous insertions and deletions
В· Split heterozygous indels into shorter and longer pseudo-alleles
В· Subtract wild type traces to reveal mutated alleles

Difference Tables:
В· Spot differences in your contigs by using the difference tables
В· Verify the differences by clicking on a cell in the difference table to navigate to a difference in the contig
В· Get an overview of all differences by looking at the condensed version of the difference table
В· Only look at differences that interest you by using filters
В· Export differences

В· Color bases by nucleotide, sequence quality, or amino acid translation
В· Hide bases that match the consensus sequence
В· Choose toolbar buttons and buttons styles
В· Fine-tune settings through extensive preferences
В· Lock, save, or load preference files
В· Use scripts to automate repetitive tasks


В· 30 days trial
В· Cannot save or print if your projects contain contigs

What's New in This Release:

Phylogenetic trees:
В· Build Neighbor-Joining trees for your contigs in CodonCode Aligner. Automatically sort your samples by distance when building a tree. You can use the phylogenetic trees as quality control for a simple way to find unexpected differences between your sequences and expected results. Rebuilding the tree after edits in a contig can help you to verify the changes. Each tree is displayed right next to your samples in the contig view. View your trees with branch lengths that represent the number of changes or see the topolgy only. You can export the phylogenetic trees in Newick format.

Contig view zooming:
В· Zoom out to view many sequences and their differences at once. Use highlighting of discrepancies and ambiguities to easily spot preserved regions. Easily identify regions with many differences, then zoom for a closer look. Changing the zoom level directly through the popup menu at the bottom left corner of the aligned bases is fast and easy.
В· Automatically shorten ...

System Requirements:

No special requirements.
Program Release Status:
Program Install Support: Install and Uninstall

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