Alignment Features in Geneious Pro™
Easily select the sequences you want to align without having to juggle files on disk or copy/paste. Click the Alignment button to begin, then quickly switch between the following array of alignment algorithms available in Geneious Pro™.
Alignment methods in Geneious Pro
- Geneious Aligner™ – Align with Needleman-Wunsch and Smith-Waterman for pairwise alignments or our own implementation of a progressive pairwise algorithm for multiple alignments
- ClustalW – Launch the power of ClustalW from inside Geneious Pro to align your DNA or protein sequences or send to a supercomputer in New Zealand via the GreenButton plugin
- MUSCLE – Choose MUSCLE from within Geneious Pro to run one of the fastest and most advanced options for iterative sequence alignment
- MAFFT – Run the new, ultra-fast and accurate alignment method for aligning DNA or protein sequences by downloading the MAFFT plugin
- Kalign – Another ultra-fast aligner, try the Kalign plugin for accurate alignments of large numbers of sequences (coming soon)
- Local re-alignment – Select a subsection of an existing alignment and re-align just those positions
- Translation Align – Create a DNA alignment based on the translated amino acid sequence, then view your original DNA sequences in a single step without ever dealing with amino acid sequence data
- Profile Align – Align new sequences to an existing alignment with profile alignment to boost the signal to noise ratio for the conserved regions of the existing alignment
- Consensus Align – Align two alignments or new sequences to an existing alignment using consensus alignment
- Mauve Genome Align – The Mauve genome alignment plugin aligns whole genomes and provides specialized visualization tool for comparing large scale differences among multiple genomes such as rearrangements, translocations and inversions based on Mauve by Aaron Darling
