plyr, phangorn, qvalue, widgetTools, calibrate, ggplot2,
R2jags, coda
Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses.

plyr, phangorn, qvalue, widgetTools, calibrate, ggplot2,
R2jags, coda, scales

plyr, phangorn, qvalue, widgetTools, calibrate, ggplot2,
R2jags, coda, scales, ape

Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses, see Budeus (2016) <doi:10.1371/journal.pone.0146409>.

Simple GUI for graph based visualization of cluster of DNA
sequence reads
SeqGrapheR package provide interactive GUI for
visualization of DNA sequence clusters. Detailes and principles
of usage are described in user manual and (2010 BMC
Bioinformatics 11:378) ,For full functionallity installed NCBI
blast is required

SeqGrapheR package provide interactive GUI for visualization of DNA sequence clusters. Details and principles of usage are described in user manual and (2010 BMC Bioinformatics 11:378) ,For full functionality installed NCBI blast is required

Simple GUI for Graph Based Visualization of Cluster of DNA
Sequence Reads
The SeqGrapheR package provide interactive GUI for visualization of DNA sequence clusters. Details and principles of usage are described in user manual and (2010 BMC Bioinformatics 11:378). For full functionality installed NCBI blast is required.