Sequence
Assembly and Mutation Detection with CodonCode Aligner
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CodonCode
Aligner is
easy-to-use program for sequence assembly, contig editing,
and mutation detection. With Aligner,
you can:
- Import sequences from ABI, SCF, and text files
- View and edit sequence traces
- Assemble or align to reference sequence
- Assemble or align in groups by name
- Align contigs with ClustalW or muscle, and go back
to the original traces by double-clicking
- Find heterozygous point mutations
- Find and analyze heterozygous insertions and deletions
- End clip
- Trim vector sequence
- Define "regions of interest" like discrepancies, low-quality
consensus sequences, or tags, and quickly navigate to these
regions
- Export sequences, assemblies, project summaries, and features
CodonCode Aligner is available
for Mac OS X and Windows. Free demo versions are available
for download.
The demo version of CodonCode Aligner is a fully functional
trace viewer and editor. Licenses for academic research are available
at a 50% discount; prices for
single-user academic licenses start at $960 . Multiple licenses
are available at substantial discounts.
New:
See
how CodonCode Aligner can accelerate your DNA sequence analysis
in Evolution research projects.
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Trace Viewing and Editing |
CodonCode offers free
programs for viewing, editing, and printing sequence traces for a number
of different operating systems:
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Mutation Detection |
CodonCode offers
two choices for mutation detection and analysis in DNA sequence traces:
- CodonCode
Aligner can find heterozygous point mutations, and find and analyze
heterozygous insertions and deletions. CodonCode
Aligner is an interactive program that also offers functions for
base calling, trace viewing and editing, sequence assembly, and
more.
CodonCode Aligner is available
for Mac OS X and Windows.
- PolyPhred is a tool to find
heterozygous mutations in "batch mode", and is well
suited for large-scale mutation analysis projects. PolyPhred
also
requires Phred for base calling and sequence assembly, and typically
is used with a contig editor like Consed or CodonCode
Aligner.
CodonCode Corporation distributes PolyPhred under license from the
University of Washingon. Academic users should obtain PolyPhred free
of charge directly
from the authors.
PolyPhred is available for UNIX,
Linux, and Mac OS X, but not for Windows.
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Base Calling |
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For base calling of
DNA sequence traces, CodonCode
distributes Phred, which many scientists
consider as the "gold standard" for base calling. Phred executables
are available for Windows, Mac OS X, Linux, and UNIX. Academic users
can obtain source code for Phred free of charge directly
from the authors.
Phred
does not provide a graphical user interface, since Phred is typically run
from automated scripts. For users who want to run Phred from a graphical
user interface, we suggest CodonCode Aligner.
CodonCode Aligner makes it easy to base call with Phred - just select
your sequence and choose "Call bases". A workstation version of Phred
is included with CodonCode Aligner. This workstation version, which can
be used only fromCodonCode Aligner, is free to academic customers. |
Sequence Assembly |
CodonCode offers
two choices for sequence assembly:
- CodonCode
Aligner supports assemblies for up to 2,000 reads from an easy-to-learn
user interface. In addition to its build-in assembly algorithm,
CodonCode Aligner can also use Phrap to generate assemblies.
CodonCode Aligner includes functions for end clipping, vector
trimming, contig editing, and
more. CodonCode
Aligner is available for Mac OS X and Windows.
- For very large assemblies, CodonCode distributes Phrap under
license from the University of Washingon. Like Phred, Phrap does
not provide a graphical user interface, since Phrap is typically
run from automated scripts. Phrap is available for Mac OS X, Windows,
Linux, and UNIX. Typically, Phrap users also need a contig editor
like Consed or CodonCode Aligner.
Academic users
can obtain source code for Phrap free of charge directly
from the authors.
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Contig Editing |
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CodonCode offers
two choices for contig editing:
- CodonCode
Aligner allows you to edit assemblies with up to 2,000 reads
from an easy-to-learn user interface on Mac OS X and Windows.
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- For contig editing on UNIX and very large assemblies, CodonCode
distributes Consed under
license from the University of Washingon. Consed is available for
Mac OS X, Linux, and UNIX. Consed is not available
for Windows.
Academic users
can obtain Consed free of charge directly
from the authors.
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