CodonCode Aligner Features

CodonCode Aligner includes the following features:

Import and Export

  • Import sequence chromatograms in ABI, AB1, or SCF format ; import text files in FASTA, FASTQ, Sam, GenBank, or EMBL format
  • Import a subset of samples (e.g. every nth sample, or only samples matching selected sequences in your project)
  • Create new text sequences and import from GenBank by accession number
  • Export sequences, consensus sequences, alignments, protein translations to SCF, FASTA, FASTQ, NEXUS/PAUP or Phylip

Sequence Editing and Trimming

  • 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

Sequence Assembly

  • 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

Sequence Alignment

  • Align to reference sequences; align cDNA to genomic DNA
  • Create Bowtie2 alignments and display paired-end reads
  • 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

Sequence Translation

  • Show the protein translation for every sequence
  • Switch back and forth between showing amino acids and bases
  • See translation-based background colors
  • Show the protein translation of your consensus sequences for annotated coding regions

Gibson Assembly

  • Virtual Gisbon Assembly with up to 15 fragments
  • Automatically pick cloning primers
  • Manually edit primers to insert e.g. spacers or to adjust the reading frame
  • Export primers directly during your experiment.

Restriction Cloning

  • Simulate your restriction cloning operations
  • View circular and linear sequence maps
  • Easily find matching overhangs for vector and insert
  • Verify your clone by looking at the reading frame

Restriction Mapping

  • 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, as text, or as virtual gel
  • Select restriction fragments by clicks on restriction maps for copying

RFLP Analysis

  • Automatically identify restriction enzymes that produce different gel lanes
  • Compare cut sites for samples in a contig
  • See and print the expected virtual gel, fragment lengths for each enzyme, or aligned samples with cut sites

Primer Design

  • Design PCR and sequencing primers
  • Create PCR primers at fixed locations for cloning
  • Primers are highlighted in your template sequence for easy recognition
  • Each primer can be imported in your project with detailed primer information
  • Export primers for ordering

Phylogenetic Trees

  • Build Neighbor-Joining trees for your contigs
  • Build trees for selected bases only to sort your samples by differences in a specific region
  • Split contigs by trees

Mutation Detection and Analysis

  • 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

Difference Tables

  • 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

Methylation Analysis

  • Analyze methylation of cytosines after bisulfite modification, PCR, and capillary sequencing from ABI data
  • View "raw" ABI trace data
  • Methylation analysis uses raw trace data, thereby avoiding artifacts from trace "normalization"
  • Get methylation results for individual sequences as well as the observed range for a contig base


This is only a partial list of features. To see what CodonCode Aligner can do, download the free trial version and use CodonCode Aligner with your own data.

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