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Hasegawa Co Ltd raxml v8 2 10
Raxml V8 2 10, supplied by Hasegawa Co Ltd, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/raxml/10+2+raxml+v8/pm41475532-103-10-17
Average 86 stars, based on 1 article reviews
raxml v8 2 10 - by Bioz Stars, 2026-10
86/100 stars

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Article Title: Phylogenomics clarifies biogeographic and evolutionary history, and conservation status of West Indian tremblers and thrashers (Aves: Mimidae).
Article Snippet: Based on the placement of Dumetella samples in the maximum likelihood tree (see Results), we also used RAxML to conduct a Shimodaira-Hasegawa (SH) test (Shimodaira and Hasegawa, 1999), comparing our best tree to a topology in which Dumetella and Ramphocinclus samples form a clade as previously hypothesized (Hunt et al. 2001, Lovette and Rubenstein, 2007; Lovette et al., 2012).

Article Title: Phylogenetic Analysis Reveals that the 'Radial Centric' Diatom Orthoseira Thwaites (Orthoseiraceae, Bacillariophyta) is a Member of a 'Multipolar' Diatom Lineage.
Article Snippet: Department of Biology, John Carroll University, University Heights, OH 44118, USA UTEX Culture Collection of Algae, Department of Molecular Biosciences, University of Texas Austin, Austin, TX 78705, USA Texas Natural Science Center, University of Texas Austin, Austin, TX 78705, USA Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice 37005, Czech Republic

Article Title: Hepatitis B Virus: Alternative phylogenetic hypotheses and its impact on molecular evolution inferences.
Article Snippet: We used RAxML to estimate the ML score this hypothesis (RAxML(F/H)), which was compared to RAxML(best) using the Shimodaira-Hasegawa test in Consel (Shimodaira & Hasegawa, 2001).

Article Title: Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria.
Article Snippet: Gobies, sleepers, and cardinalfishes represent major clades of a species rich radiation of small bodied, ecologically diverse percomorphs (Gobiaria).. Molecular phylogenetics has been crucial to resolving broad relationships of sleepers and gobies (Gobioidei), but the phylogenetic placements of cardinalfishes and nurseryfishes, as reciprocal or sequential sister clades to Gobioidei, are uncertain.. In order to evaluate relationships among and within families we used a phylogenetic data mining approach to generate densely sampled trees inclusive of all higher taxa.

Article Title: The paedomorphic lateral line system in Pseudamiops and Gymnapogon (Percomorpha, Apogonidae), with morphological and molecular-based phylogenetic considerations.
Article Snippet: Funding information Fujiwara Natural History Foundation; Japan Society for the Promotion of Science, Grant/ Award Numbers: 17H03859, 19J13664, 19K06214, 19K06810 Abstract The lateral line system and its innervation were examined in two paedomorphic species of Apogonidae, Gymnapogon japonicus and Pseudamiops cf. springeri, both of which have been included in Gymnapogonini (Apogoninae) characterized by a small translucent body lacking canalized lateral line scales, but with many superficial neuromasts (total SNs: 2,691 and 2,197 in G. japonicus and Pseudamiops cf. springeri, respectively).. Although scales are entirely absent in G. japonicus, the innervation pattern of the trunk lateral line system is basically similar to that in other apogonids having a single lateral line scale series.. In comparison, Pseudamiops cf. springeri (and P. gracilicauda) have three series of inconspicuous lateral line scales with a distinct innervation pattern, implying a phylogenetic affinity with Pseudamia (Pseudamiinae).

Sequencing:

Article Title: Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution.
Article Snippet: Specifically, a series of phylogenetic trees were built based onmultiple sequence alignment of all GRAS protein domains (including the homologous bacteria-derived SAM-dependent methyltransferase as outgroup) by RAxML (1,000 bootstrap replicates), IQ-tree (1,000 generations of Ultrafast bootstrap) and FastTree (computes local support values with the Shimodaira-Hasegawa test), respectively, implementing the Maximum Likelihood method (ML-based) with different evolutionary models (RAxML: LG4X, and GTR+CAT models; IQtree: LG4X model; FastTree: JTT + CAT model). .. Specifically, a series of phylogenetic trees were built based onmultiple sequence alignment of all GRAS protein domains (including the homologous bacteria-derived SAM-dependent methyltransferase as outgroup) by RAxML (1,000 bootstrap replicates), IQ-tree (1,000 generations of Ultrafast bootstrap) and FastTree (computes local support values with the Shimodaira-Hasegawa test), respectively, implementing the Maximum Likelihood method (ML-based) with different evolutionary models (RAxML: LG4X, and GTR+CAT models; IQtree: LG4X model; FastTree: JTT + CAT model). ..

Bacteria:

Article Title: Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution.
Article Snippet: Specifically, a series of phylogenetic trees were built based onmultiple sequence alignment of all GRAS protein domains (including the homologous bacteria-derived SAM-dependent methyltransferase as outgroup) by RAxML (1,000 bootstrap replicates), IQ-tree (1,000 generations of Ultrafast bootstrap) and FastTree (computes local support values with the Shimodaira-Hasegawa test), respectively, implementing the Maximum Likelihood method (ML-based) with different evolutionary models (RAxML: LG4X, and GTR+CAT models; IQtree: LG4X model; FastTree: JTT + CAT model). .. Specifically, a series of phylogenetic trees were built based onmultiple sequence alignment of all GRAS protein domains (including the homologous bacteria-derived SAM-dependent methyltransferase as outgroup) by RAxML (1,000 bootstrap replicates), IQ-tree (1,000 generations of Ultrafast bootstrap) and FastTree (computes local support values with the Shimodaira-Hasegawa test), respectively, implementing the Maximum Likelihood method (ML-based) with different evolutionary models (RAxML: LG4X, and GTR+CAT models; IQtree: LG4X model; FastTree: JTT + CAT model). ..

Comparison:

Article Title: Origin and evolution of papillomavirus (onco)genes and genomes
Article Snippet: .. The effect of the calibration points, and therewith forced clades, on the topology of the tree was validated by constructing an ML tree constrained to the calibrations used (electronic supplementary material, figure S1B) and subsequent comparison to the unconstrained tree using a Shimodaira–Hasegawa test [ ], as implemented in RAxML. ..



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