A Tool to Associate FASTA Sequences and Features
Finding pairs of alignment positions that jointly mutate
Finding pairs of sequence alignment positions associated with sequence...
Searches for associations of single alignment positions with feature(s...
Searches for associations of single alignment positions with feature(s...
Compare results of SeqFeatRs assocpoint with SeqFeatRs assocpair, asso...
Searches for associations of a tuple of alignment positions with featu...
Compares ancestral sequence with sequence alignment
Tries to identify a founder effect in results from SeqFeatRs assocpair
Get frequencies for amino acids/nucleotides in alignment window (epito...
Visualize odds ratios and p-values from SeqFeatRs assocpoint
Calculate q-values from p-values
Rewrite result from SeqFeatRs assoctuple
GUI for SeqFeatR
A small version of manhattan plot
Visualize association of mutation pairs and features from two (compara...
Visualize pairs of alignment positions that jointly mutate
Visualize pairs of sequence alignment positions associated with sequen...
Create volcano plot
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>.