Align

• 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.

Keywords: Manual sequence alignment editor, DNA, RNA, protein, wizard, prepare for phylogenetic analyses