Free alignment software for mac

MegAlign 7.0 is actually beneficial to offer you a choice of four pairwise and four multiple sequence alignment methods for aligning nucleic acid or polypeptide sequences. Enter your own sequences or load public data directly from NCBI*. If you want to find more related sequences for alignment, simply run a BLAST query or utilize the Entrez text query interface*, then drop in the sequences you want from the list of matches.

Easily customize views of alignments to highlight the similarities or differences of the sequences. Differences in chemical, structural or functional characteristics between sequences can also be displayed as well as your own groupings or consensi. You may create a subalignment from the current alignment by simply selecting a sub-region.

MegAlign also enables you to construct phylogenetic trees, generate detailed numerical reports or export data of sequence comparisons. Whether you want to compare gene families or sequence pairs, MegAlign provides you with flexible tools for customizing output for presentation and publication.

CLC Protein Workbench 5.1 is a useful tool which provides a wide range of advanced protein analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench.

This 2 x 2 weeks of fully functional demo includes a vast amount of advanced protein sequence analyses - all analyses are integrated in one single user-friendly and intuitive software application.

Major Features:

1. Protein sequence analysis
   • Integrated 3D molecule view
   • Transmembrane helix prediction
   • Antigenicity
   • Secondary protein structure prediction
   • PFAM domain search
   • Web-based prediction of signal peptides and their cleavage sites
   • Hydrophobicity analyses and graphs
   • Protein charge analysis and graphs
   • Reverse translation from protein to gene (a number of translation tables)
   • Interactive translations of DNA and RNA to protein (both single sequences and alignments)
   • Proteolytic cleavage detection
   • Report of protein statistics (one or more proteins in each report)
   • Comprehensive report including a range of protein analyses in one document
2. Database searches
   • Web based sequence search using BLAST
   • BLAST on local databases
   • Build local BLAST databases
   • GenBank Entrez searches
   • UniProt searches (SwissProt/TrEMBL)
   • PubMed lookup
   • Web based lookup in UniProt, NCBI, and Google
3. Pattern search
   • Search for sequence matches
   • Motif search for basic patterns
   • Motif search using regular expressions
   • Motif search with ProSite patterns
   • Pattern discovery (unknown patterns)
4. Project and data management
   • Full integration of data input, data management, calculation results, and data export
   • Detailed history log
   • All types of files can be saved in local projects, and launched from the program
   • Import and export of data in a large number of file formats
   • Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects
5. Other bioinformatics features
   • DNA, RNA and protein sequence editor displaying both linear and circular molecules
   • Multiple alignment of DNA, RNA, and proteins
   • • Two proprietary algorithms
     • ClustalW
     • Muscle
     • T-Coffee
     • MAFFT
     • Kalign
   • Joining multiple alignments into one
   • DNA, RNA, and protein alignment editor
   • Interactive logo graphs along both DNA, RNA and Protein alignments
   • Batch processing of analyses on multiple sequences in one work-step
   • Advanced re-alignment and fix-point alignment option
   • Manual annotation of sequences
   • Dot plot based analyses
   • Local complexity region analyses and complexity plots
   • Gap fraction graphs
   • G/C content analysis and graphs
   • Advanced pairwise comparison
   • Extract annotations

Enhancements:

• Better feedback on processes: there is a tool tip showing details and start time.
• Translation of DNA to protein in sequence views can now be set to follow existing CDS/ORF annotations.
• Much improved memory performance and processing time of large data sets
• Output and error log files are now placed in the application data directory in the user home
• Fixed error when parsing files from Clone Manager (cm5-files)
• UniProt search works again

Requirements:

• 3D viewing requires an OpenGL 3D graphics driver (included with almost all graphics cards)
• Mac OS X 10.4 or later (including Intel-based Macs)
• Windows 2000, Windows XP, or Windows Vista
• Linux: Redhat or SuSE
• 256 MB RAM required
• 2 GB RAM recommended
• 1024 x 768 display recommended

CLC RNA Workbench 4.2 brings you an easy way to a range of complex algorithms and options. RNA secondary structures can be predicted using state-of-the-art free energy minimization algorithms.

Major Benefits:

• You will have easy access to a large number of integrated research tools:
• • Secondary structure prediction
  • Graphical view and editing of secondary structure
  • Tabular view of structures and energy contributions
  • Symbolic representation in sequence view
• You can make your computer a High Performance Computing center
• • Unleash the hidden powers in your CPU with the Bioinformatics Cell
  • 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
  • Share data with your colleagues using CLC Database Solution
• 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 can customize your workbench
• You have the possibility to customize your workbench through our Software Developer Kit.

Major Features:

1. Bioinformatics features in CLC RNA Workbench
   • Secondary structure prediction
   • Graphical view and editing of secondary structure
   • Tabular view of structures and energy contributions
   • Symbolic representation in sequence view
2. Pattern search
   • Search for sequence matches
   • Motif search for basic patterns
   • Motif search using regular expressions
   • Motif search with ProSite patterns
   • Pattern discovery (unknown patterns)
   • Project and data management
   • Full integration of data input, data management, calculation results, and data export
   • Detailed history log
   • All types of files can be saved in local projects, and launched from the program
   • Import and export of data in a large number of file formats
   • Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects
3. Other bioinformatics features
   • DNA, RNA and protein sequence editor displaying both linear and circular molecules
   • Multiple alignment of DNA, RNA, and proteins
   • • Two proprietary algorithms
     • ClustalW
     • Muscle
     • T-Coffee
     • MAFFT
     • Kalign
   • Joining multiple alignments into one
   • DNA, RNA, and protein alignment editor
   • Interactive logo graphs along both DNA, RNA and Protein alignments
   • Batch processing of analyses on multiple sequences in one work-step
   • Advanced re-alignment and fix-point alignment option
   • Manual annotation of sequences
   • Dot plot based analyses
   • Local complexity region analyses and complexity plots
   • Gap fraction graphs
   • G/C content analysis and graphs
   • Advanced pairwise comparison
   • Extract annotations
4. Database searches
   • Web based sequence search using BLAST
   • BLAST on local databases
   • Build local BLAST databases
   • GenBank Entrez searches
   • PubMed lookup
   • Web based lookup in UniProt, NCBI, and Google

Enhancements:

• 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:
• • Fixed tblastn numbering issue
  • 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

WireframeSketcher is an Eclipse plugin for creating wireframes, UI prototypes, and screen mockups.

Enhancements
- WireframeSketcher Spy plugin. Convert SWT dialog and windows to a mockup.
- New screen wizard now has an additional page that allows to paste an initial XML content.
- Changed the look of the note widget to something more simple.
- Note widget now has text alignment property.