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28 lines
1.3 KiB
Text
28 lines
1.3 KiB
Text
MUSCLE 5: Next-generation MUSCLE
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Muscle v5 is a major re-write of MUSCLE based on new algorithms.
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* Highest accuracy, scalable to thousands of sequences:
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Compared to previous versions, Muscle v5 is much more accurate, is often
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faster, and scales to much larger datasets. At the time of writing (late
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2021), Muscle v5 has the highest scores on multiple alignment benchmarks
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including Balibase, Bralibase, Prefab and Balifam. It can align tens of
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thousands of sequences with high accuracy on a low-cost commodity
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computer (say, an 8-core Intel CPU with 32 Gb RAM). On large datasets,
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Muscle v5 is 20-30% more accurate than MAFFT and Clustal-Omega.
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* Alignment ensembles:
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Muscle v5 can generate ensembles of high-accuracy alternative
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alignments. All replicates have equal average accuracy on benchmark
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test, including the MSA made with default parameters. By comparing
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results of downstream analysis (trees, structure prediction...) on
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different replicates, you can assess the effects of alignment errors on
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your study.
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* Manual:
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https://drive5.com/muscle5/manual/
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* Reference (included in the package)
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R.C. Edgar (2021) "MUSCLE v5 enables improved estimates of phylogenetic
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tree confidence by ensemble bootstrapping"
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https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full.pdf
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