Interface to Popular Multiple Sequence Alignment Tools


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Documentation for package ‘rMSA’ version 0.99.0

Help Pages

box Boxshade: Shading Multiple Aligned Sequences
boxshade Boxshade: Shading Multiple Aligned Sequences
boxshade_help Boxshade: Shading Multiple Aligned Sequences
clustal Run Multiple Sequence Alignment (ClustalW) on a Set of Sequences
clustal_help Run Multiple Sequence Alignment (ClustalW) on a Set of Sequences
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
kalign Multiple Sequence Alignment (Kalign)
kalign_help Multiple Sequence Alignment (Kalign)
mafft Run Multiple Sequence Alignment (MAFFT) on a Set of Sequences
mafft_help Run Multiple Sequence Alignment (MAFFT) on a Set of Sequences
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
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
random_sequences Create a Set of Random Sequences
rMSA_INSTALL Installing Third-Party Software for rMSA
rMSA_install Installing Third-Party Software for rMSA
simRank Compute the SimRank Similarity between Sets of Sequences