A Tool to Associate FASTA Sequences and Features

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) .


SeqFeatR Version 0.3.1


  • getfreqs now working with only one feature

SeqFeatR Version 0.3


  • HLA input can now be 4 letter coded
  • HLA input can now include a third definition for HLA (C)

SeqFeatR Version 0.2.7


  • wrong package Rd removed

SeqFeatR Version 0.2.6


  • no loop is visible corrected

SeqFeatR Version 0.2.5


  • Own citation corrected (escaped characters)

SeqFeatR Version 0.2.4


  • Own citation added

SeqFeatR Version 0.2.3


  • small change because of new function in package ape with same name as function in Biostrings

SeqFeatR Version 0.2.2


  • new function! smallmanhattan produces small versions of the manhattan plot from assocpoint
  • correction of OR values in assocpoint function

SeqFeatR Version 0.2.1


  • phylo bias new

SeqFeatR Version 0.2.0


  • Bayes Factor for association
  • Hierarchical Bayes for association as extra function which uses R2jags and JAGS. JAGS has to be installed if you want to run assocpointhierarchical.

SeqFeatR Version 0.1.7


  • new functionality! Get frequencies for epitope positions
  • graphical results from assocpoint can be with or without possible epitope plot
  • updated man-pages

SeqFeatR Version 0.1.6


  • GUI updates
  • possibility to use Bayes as correction for assocpoint
  • OR Plot can be p-values or odds ratios now
  • new plot! volcano plot for feature association results

Reference manual

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0.3.1 by Bettina Budeus, a year ago

Browse source code at https://github.com/cran/SeqFeatR

Authors: Bettina Budeus

Documentation:   PDF Manual  

GPL (>= 3) license

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

Depends on tcltk, tcltk2, Biostrings, plotrix

Suggests xtable

See at CRAN