Geneious Basic 5.4.4

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An application that speeds up and simplifies research in molecular biology and biochemistry.



Geneious is a useful, unique and easy-to-use software system which has been designed to greatly speed up and simplify the research in molecular biology and biochemistry.Geneious is a cross-platform research engine for the retrieval, organization and analysis of biomolecular data that allows any molecular biologist do core bioinformatics tasks in a flash by removing painful data-administration. Geneious comes pre-bundled with bioinformatics functions from publication or nucleotide searching through to sequence alignment and tree-building, and includes functions for extracting protein translations, sequence analysis and 3D structure visualization.Geneious lets you set up agents to let new publications and sequences automatically find you, and eliminates the need for manually cutting and pasting sequences. It contains all core bioinformatics functions in an integrated workflow. Because Geneious agents set up a workspace with only the sequences and publications you care about, you never need to visit primary website sources again, and research can sometimes literally happen in a flash because you have circumscribed the problem of large data sets in an unwieldy format.Geneious is for any molecular biologist that wants to improve the speed and sophistication of their research by using bioinformatics approaches, but doesn't necessarily expect to be a bioinformatician.Note: Free for non-commercial use. 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 What's New in This Release: [ read full changelog ]

New features:
· Added "Whole Words Only" checkbox to local documents searching so that you can search for partial words
· Added "Find All" button when using "Find in Document" on the sequence/alignment viewer
· Can select multiple folders for moving/deleting and for showing the contents of them all at once

Bugs fixed:
· When a sequence is circularized, annotation intervals extending past the ends of the sequence are now truncated
· When a sequence is de-circularized, annotation intervals spanning the origin are split into multiple intervals
· Fixed poor performance when viewing some sequences with over 100,000 annotations
· Empty sub-folders are now kept when exporting folders
· Separate by barcode works on already paired reads and lets you choose which sequence in the pair has the barcode
· Fixed problem with garbled fonts on some systems
· Fixed de novo assembler running out of file handles on machines with lots of processors
· Greatly improved the speed at which Geneious performs large ba...
geneious-basic-5.4.4.exe 46.047 MB
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