geneious
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Geneious Version 3.5 (25 October 2007)
Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc.
It features sequence alignment and phylogenetic analysis, contig assembly, primer design and restriction analysis, access to NCBI and UniProt, BLAST, protein structure viewing, automated PubMed searching, and more.

• Windows (includes Java 1.5, Vista compatible)
• Mac OS X (Mac OS X 10.5 Leopard compatible)
• Linux (includes Java 1.5)
• Solaris

• Consensus sequence, translation and complement update as you edit
• Several pairwise and multiple sequence alignment options including Progressive pairwise and alignment of nucleotide translation
• Phylogenetic tree building with UPGMA, NJ with bootstrapping and consensus trees
• User-friendly plugin to MrBayes bayesian analysis
• Print trees for insert into your research, preserving tree-lengths.
• Find motifs, open reading frames (ORFs)

• Customizable graphical viewer and editor of sequences, alignments and annotations
• Interactive phylogenetic tree viewer with fast selection of source sequences in alignment
• Graphs updated real-time including sequence logos, chromatogram traces and protein properties
• 3D protein structure viewing
• Fast, interactive dot plots

• Contig assembly with automated trimming, assembly, and chromatogram editing
• Restriction enzyme mapping and digestion
• Design primers with ambiguities and mismatches
• Test individual primers or search a set of primers for the best matches

• Store and organize all of your research material in one place
• Collaborate and share data over the internet or on a secure, central server.
• Search and sort sequences by similarity, basic and advanced text searching of data
• Extensive import and export including Endnote, Nexus, Newick, Fasta, PDF, ABI,…
• Add your own custom notes to sequences, alignments and trees

• Drag and drop sequences from NCBI (including Gene, Genome, Nucleotide, SNP, Structure and Protein)
• Close integration with Pfam databases
• Keeps your NCBI and EMBL downloads up to date automatically
• NCBI BLAST sequences with two clicks of the mouse
• A unique method of rapidly filtering public data as it downloads

• Create interactive tutorials with direct links to material in Genieous
• All the tools a budding bioinformatician may need is just a click away
• Students can answer question, do analyses then submit their results using Collaboration

• Automatically retrieves newly published articles and can sort them based on your interests
• Storage of abstracts and bibliographic information
• Quick links to find original articles and citation record online

Drummond AJ, Ashton B, Cheung M, Heled J, Kearse M, Moir R, Stones-Havas S, Thierer T, Wilson A (2007) Geneious v3.5, Available from http://www.geneious.com/