Multiple sequence alignments are widely used to infer evolutionary relationships, enabling
inferences of structure, function, and phylogeny. Standard practice is to construct one …

Multiple sequence alignment (MSA) is an essential cornerstone in bioinformatics, which can
reveal the potential information in biological sequences, such as function, evolution and …

Phylogenetic tree confidence is often estimated from a multiple sequence alignment (MSA)
using the Felsenstein bootstrap heuristic. However, this does not account for systematic …

Motivation Currently used methods for estimating branch support in phylogenetic analyses
often rely on the classic Felsenstein's bootstrap, parametric tests, or their approximations. As …

Data on morphology, anatomy, secondary chemistry, ecology, as well as phylogenetic
reconstructions based on ITS/5.8 S and mtSSU sequence data suggest that “Flavocetraria” …

Masri M, Sukmawaty E, Aditia L. 2021. Novel chitinolytic bacteria from the shrimp shell
processing waste. Biodiversitas 22: 2672-2681. Chitinase is an enzyme that hydrolyzes …

In maximum likelihood (ML), the support for a clade can be calculated directly as the
likelihood ratio (LR) or log‐likelihood difference (S, LLD) of the best trees with and without …

Motivation The standard bootstrap method is used throughout science and engineering to
perform general-purpose non-parametric resampling and re-estimation. Among the most …

The investigation of the evolutionary history of organisms, both at the cellular level and at the
species level, is a relevant research topic in computational biology. These investigations …

Here I provide further details of the algorithm, which is only briefly described in the Methods
section due to space constraints. The primary algorithm component of Muscle5 is PPP, a re …