Free sequences software for mac

Sequence editing, reverse complement, protein translation, ORF finding, secondary structure, composition, isoelectric point, primer design, pairwise comparison, publish layout, sequence reformatting. Fetches sequence entries directly from the NCBI via Accession number or GID. Reads most sequence formats.
This (Java) application is a collage of coding projects which I have written over the past several years for various clients in my work as a bioinformatics consultant. These clients have graciously allowed me to release these works into the public domain as freeware.
Enhancements:
- Fixed launching conflict introduced with QuickTime 7.0.4
- Digest: Using "REBase 601" enzyme list
- Allow launching with Java 5 (JDK 1.5).

CLC Sequence Viewer 6.2 is a freeware that creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options.

Major Benefits:

• You will have easy access to a large number of integrated research tools:
• • Creating and editing alignments
  • Interactive restriction site analysis
  • Phylogenetics
  • Integrated GenBank searches
  • Advanced DNA to Protein translation
• You can get easy access to hardware accelerated database searches
• • Plug in the Bioinformatics Cube and increase your search speed up to 200 times
• Your research work will be easy to carry out
• • The program is graphically based, intuitive, and user-friendly
• You will have a bioinformatics solution that continuously evolves
• • The frequent program updates keep you up to date with the latest scientific developments. Your ideas for future improvements will have top priority.
• You will get superior customer service
• • Free support to all users.
    

Major Features:

1. Bioinformatics features in CLC Sequence Viewer
   • Multiple alignment of DNA, RNA, and proteins
   • • Two proprietary algorithms
     • ClustalW
     • Muscle
     • T-Coffee
     • MAFFT
     • Kalign
   • Consensus sequence determination and management
   • Conservation score along alignments
   • Open reading frame determination
   • Easy access to web-based protein and nucleotide search in GenBank, including download facilities and full graphical overview of sequence annotations of your choice
   • Translation from DNA to proteins (all genetic translation tables)
   • Reports with residue composition, molecular weight and iso electric point (for proteins)
   • Neighbor-joining and UPGMA phylogenies
   • Restriction site analysis and viewing
   • Create reverse complement
   • Shuffle sequence
   • Option of viewing and graphical manipulation of bioinformatics analyses made in commercial workbenches from CLC bio
2. Other features in CLC Sequence Viewer
   • Full integration of data input, data management, calculations results, and data export. This eliminates time spent on manual data transfers between different programs and databases
   • All types of files can be saved in local projects and launched from the program
   • Detailed history log
   • User-friendly graphical tools used in order to find and work with relevant regions of DNA, RNA and protein sequences
   • Text-based sequence view
   • Easy printing of reports and graphics
   • Export of user-defined figures to various graphics file formats
   • Import and export of data in a large number of file formats
   • Option of working with different files and in different file projects at the same time
   • Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects

Enhancemnets:

• New features:
• • Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
  • Advanced view of elements in a folder including batch editing.
  • Extract sequences improvements
  • You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)
  • "Find" in text view now accepts Enter as command to find the next hit
  • Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
  • Export of annotations in GFF format (note that annotations with joined regions are not supported)
• Bug fixes:
• • Problem rendering scatter plots without lines
  • DNA strider files could loose name upon import
  • Rare misplacement of annotations when editing very large sequences
  • Various bug-fixes

Link Sequence Downloader QED 0.21 is a good tool possessing desirable qualities in downloading a series of files, such as images and videos, to your hard-drive.

By entering a link, with ranges in square brackets - a large list of files can be downloaded in one go. For example, the Link Sequence: http://www.example.com/videos/[1-10]/vid[001-004].mpg would attempt to download forty mpeg video files; four files named vid001.mpg, vid002.mpg, vid003.mpg, vid004.mpg from each of ten folders numbered 1 to 10.

Geneious 4.8 is designed to attract users as an integrated bioinformatics tool 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 biological databases, BLAST, protein structure viewing, NCBI, EMBL, PubMed auto-find, and more. It even includes an API for creating your own plugins.

SeqMan II enables you to assemble fragment data from sequencing projects of any size - from a few fragments to tens of thousands of fragments - at the push of a button.
SeqMan II removes unreliable data, including poor quality ends, sub-minimal length reads, and vector and contaminating host sequences in a single pass, then assembles the trimmed data and calls the consensus.
Enhancements:
- Primer Walking
- SNP Discovery.

EditSeq 6.0 allows you to work on nucleic acid and protein sequences of all sizes from various popular formats. You can also utilize the integrated internet interface to search NCBI's databases to locate sequences by accession number, sequence similarity via BLAST, or keyword searches via the Entrez text query.

For your convenience, EditSeq separates the sequence, comments and annotations into three editable panes. Dynamic links between the sequence and its annotations automatically update feature coordinates when you edit a sequence and provide feature inclusion when copying/pasting sequences. Available functionality also includes the ability to reverse complement, translate, back-translate sequences and identify ORFs. As with other Lasergene applications, EditSeq will handle sequences ranging in size from a couple of nucleotides to a whole bacterial genome.