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authorPetar Petrov <slackalaxy@gmail.com>2022-10-08 18:13:17 +0100
committerWilly Sudiarto Raharjo <willysr@slackbuilds.org>2022-10-15 10:47:28 +0700
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downloadslackbuilds-1f43c07f3ce63f69512eda9410131fad0d266ea5.tar.xz
academic/muscle5: Added (MUSCLE 5: Next-generation MUSCLE)
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
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+MUSCLE 5: Next-generation MUSCLE
+
+Muscle v5 is a major re-write of MUSCLE based on new algorithms.
+
+* Highest accuracy, scalable to thousands of sequences:
+Compared to previous versions, Muscle v5 is much more accurate, is often
+faster, and scales to much larger datasets. At the time of writing (late
+2021), Muscle v5 has the highest scores on multiple alignment benchmarks
+including Balibase, Bralibase, Prefab and Balifam. It can align tens of
+thousands of sequences with high accuracy on a low-cost commodity
+computer (say, an 8-core Intel CPU with 32 Gb RAM). On large datasets,
+Muscle v5 is 20-30% more accurate than MAFFT and Clustal-Omega.
+
+* Alignment ensembles:
+Muscle v5 can generate ensembles of high-accuracy alternative
+alignments. All replicates have equal average accuracy on benchmark
+test, including the MSA made with default parameters. By comparing
+results of downstream analysis (trees, structure prediction...) on
+different replicates, you can assess the effects of alignment errors on
+your study.
+
+* Manual:
+https://drive5.com/muscle5/manual/
+
+* Reference (included in the package)
+R.C. Edgar (2021) "MUSCLE v5 enables improved estimates of phylogenetic
+tree confidence by ensemble bootstrapping"
+https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full.pdf