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|Command line
| {{Official website|www.clustal.org}}
|-
| [[CodonCode Aligner]]
| {{no | no, but can read, add & show structure annotations}}
| {{yes|[[Clustal]], MUSCLE, various built-in algorithms}}
| {{yes| Yes}}
| Multi- and pairwise alignments, assembly, sequence translation, editing, trimming, mutation detection, restriction analysis, cloning, primer design, dotplot, much more
| ABI, SCF, [[FASTA format|FASTA]], FASTQ, [[Nexus file|Nexus]]/PAUP or [[PHYLIP]], Sam, Bam, .dna, EMBL, GenBank, BLAST, GFF
| {{proprietary}}, [[Commercial software|commercial]], Viewer is [[Freeware]]
|No
|Mac OS, Windows
| {{Official website|www.codoncode.com/aligner}}
|-
| Cylindrical Alignment App
| |||