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MUSCLE Multiple Sequence Alignment (DNA) - v3.8.425


By: dylan


Build a Multiple Sequence Alignment (MSA) for nucleotide sequences using MUSCLE.

This App builds a Multiple Sequence Alignment (MSA) of nucleotide sequences with MUSCLE. MUSCLE is one of the most widely-used methods in biology. It performs an MSA and does so, according to their website, with accuracy and speed that are consistently better than CLUSTALW . The KBase implementation takes a FeatureSet object with a list of DNA references, extracts the sequences, and performs the alignment. The MSA can then be downloaded in FASTA and Clustal format. The MSA is also stored as an MSA data object in KBase for downstream analysis Apps such as FASTTREE-2 Phylogenetic Tree Builder.

The MUSCLE nucleotide app can also accept a SingleEndLibrary (e.g. 16S amplicons).

Inputs and Parameters:


Team members who implemented algorithm in KBase: Dylan Chivian. For questions, please contact us.

Related Publications

App Specification:

Module Commit: 56d38b26a1c151e2f657085e2550070fe47de541