Geneious: the easiest way to do sequence analysis
Sequence Alignment
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:
Geneious Align – For pairwise alignment this offers Needleman-Wunsch and Smith-Waterman. For multiple alignment this uses our own implementation of a progressive pairwise algorithm
MUSCLE – One of the fastest alignment implementations available today. MUSCLE is a public domain program.
ClustalW – ClustalW is a widely used program for performing sequence alignment.
Translation Align – Translates nucleotide sequences, aligns the translations using any of the above programs then back translates them for you to produce a nucleotide alignment.
Consensus Align – Aligns two alignments or adds a sequence to an alignment using their consensus sequences.
Profile Align – Aligns two alignments or adds a sequence to an alignment using alignment profiles.
Mauve Genome Align – A separate plugin available for download based on Mauve which can perform multiple alignment of bacterial genomes and includes a specialized viewer for the alignments.
Choose the parameters for any of these in an easy to use interface with no need to remember command line parameter names and what they mean. Hold your mouse over and option in Geneious and you will be given the description for that parameter in a pop-up.
Once your alignment is complete you can visualize the results in many different ways without having to load up any other programs, Geneious offers the right viewers for your data automatically including:
- View annotations such as exons and transcription binding sites and easily copy them between sequences
- sequence similarity plots, hydrophobicity for protein sequence alignments and sequence logo graphs
- dot plots
- phylogenetic tree diplayed in combination with alignment
Phylogenetic Tree Building
Building a tree is just as easy as building an alignment. Without having to launch a new program you can just click on the alignment produced by any of the algorithms above and click the Tree button to begin. Geneious offers the following algorithms:
Neighbor Joining – Geneious includes a built in implementation of basic tree building using NJ, UPGMA and options to bootstrap and build a consensus tree.
PAUP* – A separate plugin available for download which runs the highly respected program PAUP* which performs Maximum Parsimony, Maximum Likelihood and Neighbor Joining. PAUP* must be purchased separately to use this plugin.
MrBayes – A separate plugin available for download which runs the widely used program MrBayes for Bayesian inference of phylogeny. This includes an array of viewers for analyzing posterior statistics that are produced by MrBayes.
PhyML – A separate plugin available for download which runs the program PhyML for maximum likelihood tree building.
Once you tree is built, view it in the interactive tree viewer, save it to a high quality vector format for publication or print it so you can stick it on the wall – all without switching away from Geneious.