Here are some key features of "CodonCode Aligner":

Import and Export:
· 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

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
· 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

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 or as text
· Select restriction fragments by clicks on restriction maps for copying

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

Customization:
· 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