Geneious Pro 4.8.3

Geneious Pro 4.8.3 is a well designed and useful bioinformatics software suite that can be used 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 cloning, access to NCBI and UniProt, BLAST, protein structure viewing, automated PubMed searching, and more. It even includes an API for creating your own plugins.

Major Features:

1. Sequence Analysis:
   • Pairwise and multiple sequence alignment including ClustalW, MUSCLE, Progressive pairwise and translation alignment
   • Phylogenetic tree building with NJ, bootstrapping, consensus trees and plugins for PAUP* and MrBayes
   • Consensus sequence, translation, complement and protein statistics update as you edit
   • Find motifs, open reading frames (ORFs) and More
2. Lab End Sequence Analysis:
   • Contig assembly with automated trimming, vector screening, assembly, and chromatogram editing
   • 454 import and reference assembly with support for viewing large assemblies
   • Restriction and Gateway® Cloning, restriction mapping, digestion and ligation
   • Automated primer design with degeneracy support
   • Keep a primer database and search for primers which match new sequences. More...
3. Sequence Visualization:
   • Customizable graphical viewer and editor of sequences, alignments and annotations
   • Fully interactive, customizable plasmid maps
   • Navigate chromosomes and genomes
   • Phylogenetic tree viewer with customizable layout, color and style
   • Graphs updated real-time including sequence logos, chromatogram traces and protein properties
   • 3D protein structure viewing
   • Fast, interactive dot plots
   • Easy image export to publication quality formats and More...
4. Organize and share data:
   • Store and organize all of your research material in one place including sequences, publications, trees and more
   • Extensive import and export including Vector NTI, Nexus, GenBank, Fasta, PDF, ABI and many more!
   • 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
   • Attach structured information to sequences, alignments and trees.
5. Access public databases:
   • Drag and drop sequences from NCBI (including Gene, Genome, Nucleotide, SNP, Structure and Protein)
   • NCBI BLAST sequences with two clicks of the mouse
   • Keeps your NCBI and EMBL downloads up to date automatically
   • Close integration with Pfam databases
   • A unique method of rapidly filtering public data as it downloads. More...
6. Teach Bioinformatics:
   • Create interactive tutorials with direct links to material in Geneious
   • 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.
7. Manage references:
   • Automatically retrieves newly published articles from PubMed and can sort them based on your interests
   • Storage of abstracts and bibliographic information
   • Quick links to find original articles and citation record online

Enhancements:

• Ultra-fast de novo assembler
• Primer extension support
• Primer design on alignments and assemblies
• Map primer to sequence
• Trim by primers
• Batch export
• Import FastQ, CsFasta, Qual file formats
• Add, remove and combine enzymes from lists
• Find in translated sequence
• Quality statistics on chromatograms
• Statistics: read length and chromatogram quality
• Bundled EMBOSS Tools