Category: Software → Geneious Basic 5.3.4

Here are some key features of "Geneious Basic":

Organize and visualize:
· Organize, visualize and search sequences (with annotations), alignments, phylogenetic trees, publications, protein structures and more!

Database integration:
· Seamlessly integrated searching with Genbank, PubMed, BLAST and UniProt

Align and build trees:
· Basic pairwise alignment, multiple alignment and tree building methods including bootstrapping and consensus trees.

Import and Export:
· Import and export Newick, Nexus, FASTA and Endnote formats. Import PDF, 3D Structures, Vector NTI, Chromatograms, DNA Strider, Clustal, list of formats

Plugins:
· Free plugins for extended functionality, Public Java API (application programming interface) for developing your own plugins

Requirements:

· Java Runtime Environment 1.5

Limitations:

· Advanced sequence viewing – Circular sequences and plasmid mapping. Consensus, translation and complement along-side sequences.
· Contig assembly – Automated contig assembly, sequence trimming, vector screening and easy contig editing
· Primers – designing and testing, degenerate primers, mismatches and multiple primer searching. (Includes software developed by the Whitehead Institute for Biomedical Research)
· Cloning – One-step insertion into a plasmid, find and view restriction cut sites, perform restriction enzyme digests and ligate fragments.
· Sequence editing – Edit sequences, sequence alignments and annotations
· Collaborate – Share documents and chat with other users of Geneious Pro from anywhere in the world
· Server Data Storage – Store data on a secure relational database (SQL, Oracle etc.) where multiple users can work with the data concurrently.
· Agents and smart agents – Agents keep your data up to date while smart agents learn about the documents you are interested in and find more for you!
· Sequence graphs – Sequence logo graph, view and edit chromatogram sequences.
· Extended connectivity – Create custom BLAST databases. Seamless integration with Pfam, NCBI Gene and NCBI SNP databases.
· Advanced alignment – MUSCLE, ClustalW, translation aignment, profile alignment and consensus alignment
· Pro only Plugins – PAUP*, EMBOSS, Mauve genome alignment and more
· Motifs and ORFs – Quickly identify and annotate motifs and open reading frames
· Geneious education – Create and use interactive tutorials for learning within Geneious
· Interoperability – Import formats from other tools like DNAStar, PIR, EMBL, GCG and Phylip, list of formats
· Chromosome viewing – Load, view, edit full human chromosomes or up to 10,000 HIV genomes
· Publication images – Publication quality image export to vector graphic formats.