Man pages for michalstolarczyk/BALCONY
Better ALignment CONsensus analYsis

alignmentSample alignment of soluable epoxide hydrolase family
alignment2matrixConvert alignment object to a matrix
align_seq_mtx2grsConvert amino acid symbols to groups according to their...
barplotshowCreates barplot with amino acid variation on the specified...
calculate_AA_variationCalculate AA variations on each position of the multiple...
calculate_pseudo_countsCalculate pseudo counts for alignment
compare_cons_metricsCompare conservation metrics
cons2seqs_identCalculate identity of each sequence in the alignment to the...
cons2seqs_simGroup consensus to each sequence in the alignment similarity
consensusDetermine consensus sequence
convert_AA_symbolAmino acids symbols conversion
create_final_CSVCreate CSV file to save results
create_structure_seqSuperimpose structural data of interest on sequence after the...
CRE_conservativityCalculate cumulative relative entropy score
delete_isoformsDelete protein isoforms from alignment object
D_matrixCalculate substitution rate matrix between two amino acids
dot-apply_pseudocounts_positionapply the pseudocounts to the position
Escore_conservativityCalculate the Escore conservation metric
excl_low_prob_strctsExclude low probability structural data
find_consecutive_seqFind sequences of numbers in a numeric vector
find_seqGet sequence by id in alignment.
find_seqidGet sequence identifier by other sequence identifier in given...
get_align_paramsGet alignment dimensions
get_pos_based_seq_weightsGet position based weights of sequences in alignment
get_prot_entropyGet MSA-based calculated entropy for chosen protein
get_remarks465_pdbGet "REMARK 465" data from PDB file
get_seq_weightsGet sequences weights
get_structures_entropyGet entropy of amino acids (for region of interest) in given...
get_structures_idxGet IDs of structure(s) elements from aligned sequences (MSA)
gonnetGonnet substitution matrix
kabat_conservativityCalculate Kabat conservation metric
kolmogorov_smirnov_testPerform Kolmogorov-Smirnov test for structural data
landgraf_conservativityCalculate Landgraf conservation score
noteworthy_seqsFind noteworthy sequences in the dataset (aligned sequences)
pairwise_alignment_MSACalculate pairwise alignment for whole MSA
plot_entropyPlot entropies for protein
plot_structure_on_proteinPlot structure entropy on protein background
prepare_structure_profileCombine the entropy data for structure building amino acids...
read_structureRead structure data from a text file
RealValET_conservativityCalculate real-value Evolutionary Trace (ET)
schneider_conservativityCalculate Schneider conservation metric
shannon_conservativityCalculate Shannon conservation metric
small_alignmentSample small alignment of soluable epoxide hydrolase family
structureSample structure data
substitution_mtxRead a substitution matrix
michalstolarczyk/BALCONY documentation built on May 7, 2019, 6:08 a.m.