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Start Your TrialMUSCLE is widely-used software for making multiple alignments of biological sequences. This version is highly scalable, with parallel capabilities and a new efficeitn algorithm called Super5. Version 5 of MUSCLE achieves highest scores on Balibase, Bralibase and Balifam benchmark tests and scales to thousands of sequences on a commodity desktop computer. Muscle5 supports generating an ensemble of alternative alignments with the same high accuracy obtained with default parameters. By comparing downstream predictions from different alignments, such as trees, a biologist can evaluation the robustness of conclusions against alignment errors.
A manual for MUSCLE5 is available.
MUSCLE home page here.
INPUT = dna or protein sequences in fasta format.
Test input file (nucleic acid): muscle_seq_in.fasta
If you use MUSCLE, please cite: Edgar, RC (2021), MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping, bioRxiv 2021.06.20.449169.]
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