- #Adding features to sequence in codoncode aligner how to#
- #Adding features to sequence in codoncode aligner movie#
- #Adding features to sequence in codoncode aligner manual#
- #Adding features to sequence in codoncode aligner windows 8#
#Adding features to sequence in codoncode aligner how to#
This section of the quick tour shows how to open and use contig views and two related views, the trace view and the quality view.
#Adding features to sequence in codoncode aligner movie#
Interested? Watch the movie showing the new features of CodonCode Aligner 4.Quick Tour: The Contig View The Contig View
#Adding features to sequence in codoncode aligner windows 8#
Improved speed and memory use during assemblies and alignmentsĬodonCode Aligner 4.1 is compatible with Windows 8 and OS X Mountain Lion (10.8).Assemble and align Next Generation Sequencing data.Tip of the Day: Look at the "Tip of the Day" in the Help menu to find out about different functionalities in CodonCode Aligner.New project format: CodonCode Aligner now saves your projects in one file, thus being faster and more memory efficient when reading and writing many sequences.Add tags to all samples: Add the same tag to all samples of a contig at the same time.Read sam files: Import your sequences in sam format.Read & write fastq files: Import and export your sequences in fastq format.Import a subset of samples: Import every nth sequence or only those samples that match the selected sequences in your project.And assemblies and alignments were adapted to work with more sequences and larger contigs. Importing subsets allows to import only sequences that share a certain amount of words with selected sequences in your project, thus enabling the user to import only certain samples from a large dataset. New file formats like fastq, and sam files enable users to import and export their data in common formats. The new project format allows for a much larger amount of data and is faster when reading and writing your projects. The new overview allows to easily work with larger projects and makes it easier to see how your sequences align and where they differ.
#Adding features to sequence in codoncode aligner manual#
Highlight your sequences, contigs and manual folders in the project view with colored labels:ĬodonCode Aligner now also has support for anlayzing & viewing NGS data. The coverage panel above the sample arrows shows colored discrepancies (with a settable threshold) and allows for fast navigation to any region of interest.īuild Neighbor-Joining trees for selected bases only which enables the user to sort samples by similarity in a selected region of the contig.Ĭontigs can be split into two new contigs by removing a branch of their tree.Īdditional options when building Neighbor-Joining trees to include internal gaps or all gaps when calculating differences. The overview allows for zooming with a zoom scale and shows which range is displayed. Mouse overs show significant information for each position, and when zooming in on the samples, discrepancies are shown in colors on the sample arrows. An improved display of the sample arrows allows the user to get a better idea of gaps and sample position in alignments. The new overview for contigs in CodonCode Aligner was optimized for large projets. On 64-bit versions of Windows, CodonCode Aligner 4.2.1 can now use memory beyond the 1.4 GB limit on 32-bit Windows, up to the available amount of physical memory (RAM). It is comatible with Windows 8 and OS X Mountain Lion (10.8).ĬodonCode Aligner 4.2 introduces support for 64-bit Windows. CodonCode Aligner version 4.0 introduces support for Next Generation Sequencing and several new features and improvements like a new contig overview, building trees for selections, splitting contigs using trees, highlighting sequences with labels, reading and writing new file formats, importing subsets, and much more.ĬodonCode Aligner 4.1 added new filters for the difference table and the option to switch between a stacked and packed overview for aligned samples.
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