Tools based on Biostrings (alignment, classification, database)


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Documentation for package ‘BioTools’ version 0.0-3

Help Pages

.getWhere Classification Hierarchy for Sequences
.pmatchRank Classification Hierarchy for Sequences
addSequences Genetic Sequences
Annotation_Greengenes Genetic Sequences
Annotation_Id Genetic Sequences
Annotation_RDP Genetic Sequences
BioTools_Software_Wizard Software Installation Wizard for BioTools
BLAST Basic Local Alignment Search Tool (BLAST)
BLAST_help Basic Local Alignment Search Tool (BLAST)
box Boxshade: Shading Multiple Aligned Sequences
boxshade Boxshade: Shading Multiple Aligned Sequences
boxshade_help Boxshade: Shading Multiple Aligned Sequences
c2s Genetic Sequences
closeGenDB Gene Sequence databases
clustal Run Multiple Sequence Alignment (clustal) on a Set of Sequences
clustal_help Run Multiple Sequence Alignment (clustal) on a Set of Sequences
createGenDB Gene Sequence databases
distAlignment Calculate Distances between Sets of Sequences
distApe Calculate Distances between Sets of Sequences
distCV Calculate Distances between Sets of Sequences
distEdit Calculate Distances between Sets of Sequences
distFFP Calculate Distances between Sets of Sequences
distKMer Calculate Distances between Sets of Sequences
distNSV Calculate Distances between Sets of Sequences
distSimRank Calculate Distances between Sets of Sequences
dropTableGenDB Gene Sequence databases
findAccuracy Ribosomal Database Project (RDP) Classifier for 16S rRNA
GenClass16S Manage GenClass16S objects
GenClass16S_Greengenes Manage GenClass16S objects
GenDB Gene Sequence databases
GenDB_Greengenes Manage GenClass16S objects
GenDB_Hierarchy Classification Hierarchy for Sequences
GenDB_Sequences Genetic Sequences
getHierarchy Classification Hierarchy for Sequences
getIDs Classification Hierarchy for Sequences
getRank Classification Hierarchy for Sequences
getSequences Genetic Sequences
getTaxonomyNames Classification Hierarchy for Sequences
kalign Multiple Sequence Alignment (kalign)
kalign_help Multiple Sequence Alignment (kalign)
listGenDB Gene Sequence databases
mafft Run Multiple Sequence Alignment (MAFFT) on a Set of Sequences
mafft_help Run Multiple Sequence Alignment (MAFFT) on a Set of Sequences
metaGenDB Gene Sequence databases
MUSCLE Run Multiple Sequence Alignment (MUSCLE) on a Set of Sequences
MUSCLE_help Run Multiple Sequence Alignment (MUSCLE) on a Set of Sequences
mutations Creates Random Mutations of a Sequence
nSequences Genetic Sequences
openGenDB Gene Sequence databases
plot Plot Genetic Sequences and Alignments
plot.DNAMultipleAlignment Plot Genetic Sequences and Alignments
plot.DNAStringSet Plot Genetic Sequences and Alignments
plot.RNAMultipleAlignment Plot Genetic Sequences and Alignments
plot.RNAStringSet Plot Genetic Sequences and Alignments
predict Ribosomal Database Project (RDP) Classifier for 16S rRNA
predict.BLAST Basic Local Alignment Search Tool (BLAST)
predict.RDPClassifier Ribosomal Database Project (RDP) Classifier for 16S rRNA
print.BLAST Basic Local Alignment Search Tool (BLAST)
print.GenDB Gene Sequence databases
print.RDPClassifier Ribosomal Database Project (RDP) Classifier for 16S rRNA
random_sequences Create a Set of Random Sequences
RDP Ribosomal Database Project (RDP) Classifier for 16S rRNA
removeRDP Ribosomal Database Project (RDP) Classifier for 16S rRNA
reopenGenDB Gene Sequence databases
s2c Genetic Sequences
Sequences Genetic Sequences
simRank Compute the SimRank Similarity between Sets of Sequences
trainRDP Ribosomal Database Project (RDP) Classifier for 16S rRNA