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Report SpywareCodonCode Aligner 3.0.1
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Software Description:
CodonCode Aligner - Fast, powerful & affordable sequence assembly, alignment, and mutation detection
Sequence assembly with CodonCode Aligner - better, faster, cheaper.
CodonCode Aligner is a leading software program for DNA sequence assembly, alignment, contig editing, and mutation detection. In addition to features common in sequence assembly programs like end clipping, alignments to reference sequences, and exporting, CodonCode Aligner offers many unique features not found in other software.
Advanced CodonCode Aligner features include:
- Assemble by name: build hundreds of contigs in seconds, based on sample names
- Accurate consensus sequences based on sequence qualities eliminate the need to edit trivial discrepancies
- Contigs of contigs: align contigs to each other with ClustalW, and go back to the underlying traces with a simple double-click
- Automate with one-step processing and scripts
- Sensitive mutation analysis with unique tools for analyzing heterozygous insertions and deletions
- Use leading tools like Clustal, MUSCLE, Phred & Phrap within CodonCode Aligner
- Get a better look at your ABI sequences with CodonCode Aligner's trace sharpening
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.
The download is a trial version that is fully functional for 30 days. It can be converted into a full version by purchasing a license. Licenses for CodonCode Aligner are substantially less expensive than licenses for comparable software packages. "Floating" licenses are available at no additional cost, and can be shared between Windows and Mac OS X.
Sequence assembly with CodonCode Aligner - better, faster, cheaper.
CodonCode Aligner is a leading software program for DNA sequence assembly, alignment, contig editing, and mutation detection. In addition to features common in sequence assembly programs like end clipping, alignments to reference sequences, and exporting, CodonCode Aligner offers many unique features not found in other software.
Advanced CodonCode Aligner features include:
- Assemble by name: build hundreds of contigs in seconds, based on sample names
- Accurate consensus sequences based on sequence qualities eliminate the need to edit trivial discrepancies
- Contigs of contigs: align contigs to each other with ClustalW, and go back to the underlying traces with a simple double-click
- Automate with one-step processing and scripts
- Sensitive mutation analysis with unique tools for analyzing heterozygous insertions and deletions
- Use leading tools like Clustal, MUSCLE, Phred & Phrap within CodonCode Aligner
- Get a better look at your ABI sequences with CodonCode Aligner's trace sharpening
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.
The download is a trial version that is fully functional for 30 days. It can be converted into a full version by purchasing a license. Licenses for CodonCode Aligner are substantially less expensive than licenses for comparable software packages. "Floating" licenses are available at no additional cost, and can be shared between Windows and Mac OS X.
Feature List:
- Import sequence chromatograms in ABI, AB1, or SCF format ; import text files in FASTA, GenBank, or EMBL format
- Create new text sequences and import from GenBank by accession number
- Export sequences, consensus sequences, alignments, protein translations to SCF, FASTA, NEXUS/PAUP or Phylip
- Manual editing of sequences and contigs, including delete to sample or contig end and contig splitting
- Automated editing tools: call or remove ambiguities, match consensus, convert low quality bases to N, undo auto-edits
- Fast navigation with toolbar buttons or keyboard shortcuts; user-definable regions of interest
- End clip to remove low quality sequence; remove vector contamination
- Assemble fragments using local, end-to-end, or large gap (cDNA to genomic) algorithms
- Accurate, quality base consensus sequences minimize the need for manual editing
- Assembly by name to build separate contigs for many clones or specimen
- Assemble with Phrap
- Align to reference sequences; align cDNA to genomic DNA
- Build 'contigs of contigs': align contigs to each other with MUSCLE or Clustal
- Go back from the contig alignment to the original traces with a double-click
- Edit the sequence traces, the contig view, or the alignment of contigs, while keeping your data consistency
- Build restriction maps using any combination of restriction enzymes
- Select by size of recognition site, overhang, cut frequency, of manufacturer
- View as single-line or multi-line maps or as text
- Select restriction fragments by clicks on restriction maps for copying
- Call secondary peaks in sequence traces
- Sensitive detection of heterozygous SNPs in assembled or aligned contigs
- View and export amino-acid level effects of mutations
- Accurate and sensitive detection of heterozygous insertions and deletions
- Split heterozygous indels into shorter and longer pseudo-alleles
- Subtract wild type traces to reveal mutated alleles
- Spot differences in your contigs by using the difference tables
- Verify the differences by clicking on a cell in the difference table to navigate to a difference in the contig
- Get an overview of all differences by looking at the condensed version of the difference table
- Only look at differences that interest you by using filters
- Export differences
- Color bases by nucleotide, sequence quality, or amino acid translation
- Hide bases that match the consensus sequence
- Choose toolbar buttons and buttons styles
- Fine-tune settings through extensive preferences
- Lock, save, or load preference files
- Use scripts to automate repetitive tasks
100% Clean:
CodonCode Aligner 3.0.1 is 100% cleanThis download (Aligner_Installer.exe) was tested thoroughly and was found 100% clean. Click "Report Spyware" link on the top if you found this software contains any form of malware, including but not limited to: spyware, viruses, trojans and backdoors.
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