clonalframe
inference of bacterial microevolution using multilocus sequence data
Command lineScience
Not tested on a device yet. What that means
Commands in the package
ClonalFrame
About clonalframe
From Debian's package description
ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.
ClonalFrame can be applied to any kind of sequence data, from a single fragment of DNA to whole genomes. It is well suited for the analysis of MLST data, where 7 gene fragments have been sequenced, but becomes progressively more powerful as the sequenced regions increase in length and number up to whole genomes. However, it requires the sequences to be aligned. If you have genomic data that is not aligned, it is recommend to use Mauve which produces alignment of whole bacterial genomes in exactly the format required for analysis with ClonalFrame.
From Debian's description of the clonalframe package, under that package's license.
Dependencies
Depends on
libc6libgcc-s1libgsl28libstdc++6
Related apps
- FastQC quality controlquality control for high throughput sequence data
- salmidrapid Kmer based Salmonella identifier from sequence dataCommand line
- prodigalMicrobial (bacterial and archaeal) gene finding programCommand line
- bitseqBayesian Inference of Transcripts from Sequencing DataCommand line
- vttoolset for short variant discovery in genetic sequence dataCommand line
- estscanORF-independent detector of coding DNA sequencesCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the clonalframe package, under that package's license.
- Description: Debian's description of the clonalframe package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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