Align - Manual DNA sequence alignment editor

Alignment of DNA sequence, RNA sequence, protein sequence and other data
Imports and exports various sequence file formats, e.g. Paup-Nexus, Phylip, Fasta, EMBL, GenBank, DCSE, and others.


  • Find/Highlight sequence motives in your molecular sequence alignment (including wildcards ? or *)
  • Wizard for automatic processing of sequence alignments for phylogenetic analyses
  • Define phylogenetic masks: Which sites are good for phylogenetic analysis?
  • Select/Deselect sequences and save selection profiles to define subsets.
  • Sort sequences by: accession numbers, taxonomy, arrangement in a phylogentic tree and others
  • Several cursor shapes: normal, exclusive (edits all sequences except cursor position), ex- and insertional, left-ended cursor
  • Change the cursor to edit several sequences simulataneously
  • Analyze sequences and alignments: similarities, p-distances, RASA, ...
  • Manipulate aligned sequences: Translate DNA/RNAs to protein using your own codon usage table
  • Cut aligned sequences: e.g. remove common positions, where a mask sequence contains special characters
  • Create sequences: e.g. consensus sequences, frequency of characters, sites that are only present in selected species (signatures), ...
  • Full access to all GenBank fields
  • Batch replacement of accession numbers by other fields in foreign files, e.g. replace labels in a tree file. This is not necessary if you have TreeMe.
  • ... and many other features.
Software Link:  Align - Manual DNA sequence alignment editor

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