UFBoot2: improving the ultrafast bootstrap approximation

DT Hoang, O Chernomor… - Molecular biology …, 2018 - academic.oup.com
The standard bootstrap (SBS), despite being computationally intensive, is widely used in
maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap …

Ultrafast approximation for phylogenetic bootstrap

BQ Minh, MAT Nguyen… - Molecular biology and …, 2013 - academic.oup.com
Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the
clade support of phylogenetic trees. However, with the rapidly growing amount of data, this …

[HTML][HTML] MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation

DT Hoang, LS Vinh, T Flouri, A Stamatakis… - BMC evolutionary …, 2018 - Springer
Background The nonparametric bootstrap is widely used to measure the branch support of
phylogenetic trees. However, bootstrapping is computationally expensive and remains a …

Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes

M Anisimova, M Gil, JF Dufayard, C Dessimoz… - Systematic …, 2011 - academic.oup.com
Phylogenetic inference and evaluating support for inferred relationships is at the core of
many studies testing evolutionary hypotheses. Despite the popularity of nonparametric …

How many bootstrap replicates are necessary?

ND Pattengale, M Alipour… - Journal of …, 2010 - liebertpub.com
Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on
phylogenetic trees that is based on reconstructing many trees from minor variations of the …

MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping

RC Edgar - BioRxiv, 2021 - biorxiv.org
Phylogenetic tree confidence is often estimated from a multiple sequence alignment (MSA)
using the Felsenstein bootstrap heuristic. However, this does not account for systematic …

How many bootstrap replicates are necessary?

ND Pattengale, M Alipour… - … Molecular Biology: 13th …, 2009 - Springer
Phylogenetic Bootstrapping (BS) is a standard technique for inferring confidence values on
phylogenetic trees that is based on reconstructing many trees from minor variations of the …

A rapid bootstrap algorithm for the RAxML web servers

A Stamatakis, P Hoover, J Rougemont - Systematic biology, 2008 - academic.oup.com
Despite recent advances achieved by application of high-performance computing methods
and novel algorithmic techniques to maximum likelihood (ML)-based inference programs …

Renewing Felsenstein's phylogenetic bootstrap in the era of big data

F Lemoine, JB Domelevo Entfellner, E Wilkinson… - Nature, 2018 - nature.com
Felsenstein's application of the bootstrap method to evolutionary trees is one of the most
cited scientific papers of all time. The bootstrap method, which is based on resampling and …

[HTML][HTML] RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation

K Liu, CR Linder, T Warnow - PloS one, 2011 - journals.plos.org
Statistical methods for phylogeny estimation, especially maximum likelihood (ML), offer high
accuracy with excellent theoretical properties. However, RAxML, the current leading method …