RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

Kozlov, Alexey M; Darriba, Diego; Flouri, Tomáš; Morel, Benoît; Stamatakis, Alexandros

doi:10.1093/bioinformatics/btz305

Cited by 2,761 publications

(2,175 citation statements)

References 19 publications

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“…These 2,311 sequences were aligned with mafft (‐‐retree 2 ‐‐maxiterate 1,000) and trimmed with trimal (‐gt 0.3 ‐st 0.001), resulting in a multiple sequence alignment (referred to as MSA) with 1,589 alignment sites. The best unconstrained ML tree was selected from 20 tree searches run using RAxML‐NG (version 0.6.0) (Kozlov, Darriba, Flouri, Morel, & Stamatakis, ). We assumed that the SILVA taxonomy is correct and consistent with the exception of a few cases—preliminary tree searches detected several potentially mislabelled RS, which were relabelled after careful inspection.…”

Section: Methodsmentioning

confidence: 99%

Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

Jamy

Foster

Barbera

et al. 2019

Molecular Ecology Resources

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High‐throughput DNA metabarcoding of amplicon sizes below 500 bp has revolutionized the analysis of environmental microbial diversity. However, these short regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. This lesser phylogenetic resolution of short amplicons may be overcome by new long‐read sequencing technologies. To test this idea, we amplified soil DNA and used PacBio Circular Consensus Sequencing (CCS) to obtain an ~4500‐bp region spanning most of the eukaryotic small subunit (18S) and large subunit (28S) ribosomal DNA genes. We first treated the CCS reads with a novel curation workflow, generating 650 high‐quality operational taxonomic units (OTUs) containing the physically linked 18S and 28S regions. To assign taxonomy to these OTUs, we developed a phylogeny‐aware approach based on the 18S region that showed greater accuracy and sensitivity than similarity‐based methods. The taxonomically annotated OTUs were then combined with available 18S and 28S reference sequences to infer a well‐resolved phylogeny spanning all major groups of eukaryotes, allowing us to accurately derive the evolutionary origin of environmental diversity. A total of 1,019 sequences were included, of which a majority (58%) corresponded to the new long environmental OTUs. The long reads also allowed us to directly investigate the relationships among environmental sequences themselves, which represents a key advantage over the placement of short reads on a reference phylogeny. Together, our results show that long amplicons can be treated in a full phylogenetic framework to provide greater taxonomic resolution and a robust evolutionary perspective to environmental DNA.

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Section: Methodsmentioning

confidence: 99%

Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

Jamy

Foster

Barbera

et al. 2019

Molecular Ecology Resources

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“…For all datasets, OGs were then aligned using Mafft v7.310 (Katoh & Standley, ) (par: ‐maxiterate 1,000 ‐‐localpair), concatenated and trimmed using trimAI v1.4.1 (Capella‐Gutierrez, Silla‐Martinez, & Gabaldon, ) with the gappyout parameter. Phylogenetic trees were inferred using RaXML‐NG v0.9.0 (Kozlov, Darriba, Flouri, Morel, & Stamatakis, ) (‐‐model LG + G8 + F ‐‐seed 15,826 ‐‐all ‐‐bs‐trees 100). The differences in topology were visualized using Phylo.io (Robinson, Dylus, & Dessimoz, ).…”

Section: Methodsmentioning

confidence: 99%

“…Phylogenetic trees were inferred using RaXML-NG v0.9.0 (Kozlov, Darriba, Flouri, Morel, & Stamatakis, 2019) (--model LG + G8 + F --seed 15,826 --all --bs-trees 100). The differences in topology were visualized using Phylo.io (Robinson, Dylus, & Dessimoz, 2016).…”

Section: Phylogenetic Tree Inferencementioning

confidence: 99%

New genome assembly of the barn owl (Tyto alba alba)

Ducrest

Neuenschwander

Schmid‐Siegert

et al. 2020

Ecology and Evolution

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New genomic tools open doors to study ecology, evolution, and population genomics of wild animals. For the Barn owl species complex, a cosmopolitan nocturnal raptor, a very fragmented draft genome was assembled for the American species (Tyto furcata pratincola) (Jarvis et al. 2014). To improve the genome, we assembled de novo Illumina and Pacific Biosciences (PacBio) long reads sequences of its European counterpart (Tyto alba alba). This genome assembly of 1.219 Gbp comprises 21,509 scaffolds and results in a N50 of 4,615,526 bp. BUSCO (Universal Single‐Copy Orthologs) analysis revealed an assembly completeness of 94.8% with only 1.8% of the genes missing out of 4,915 avian orthologs searched, a proportion similar to that found in the genomes of the zebra finch (Taeniopygia guttata) or the collared flycatcher (Ficedula albicollis). By mapping the reads of the female American barn owl to the male European barn owl reads, we detected several structural variants and identified 70 Mbp of the Z chromosome. The barn owl scaffolds were further mapped to the chromosomes of the zebra finch. In addition, the completeness of the European barn owl genome is demonstrated with 94 of 128 proteins missing in the chicken genome retrieved in the European barn owl transcripts. This improved genome will help future barn owl population genomic investigations.

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“…Multiple sequence (nucleotide) alignments were generated using the default settings in MUSCLEv3.8.1551 [65], and ModelTest-NGv0.1.5 was used to identify the best-fitting evolutionary model. Using the best-fitting model of for evolution, we reconstructed a maximum-likelihood phylogeny using RAxML-ng v0.6.0 using default settings [66]. Annotation of protein domains in the novel orthobunyavirus was performed using the InterPro webserver [67] as well as direct alignment against previously known orthobunyaviruses.…”

Section: Genome Assembly Annotation and Phylogenetic Analysismentioning

confidence: 99%

Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda

et al. 2019

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Febrile illness is a major burden in African children, and non-malarial causes of fever are uncertain. In this retrospective exploratory study, we used metagenomic next-generation sequencing (mNGS) to evaluate serum, nasopharyngeal, and stool specimens from 94 children (aged 2–54 months) with febrile illness admitted to Tororo District Hospital, Uganda. The most common microbes identified were Plasmodium falciparum (51.1% of samples) and parvovirus B19 (4.4%) from serum; human rhinoviruses A and C (40%), respiratory syncytial virus (10%), and human herpesvirus 5 (10%) from nasopharyngeal swabs; and rotavirus A (50% of those with diarrhea) from stool. We also report the near complete genome of a highly divergent orthobunyavirus, tentatively named Nyangole virus, identified from the serum of a child diagnosed with malaria and pneumonia, a Bwamba orthobunyavirus in the nasopharynx of a child with rash and sepsis, and the genomes of two novel human rhinovirus C species. In this retrospective exploratory study, mNGS identified multiple potential pathogens, including 3 new viral species, associated with fever in Ugandan children.

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RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

Cited by 2,761 publications

References 19 publications

Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

New genome assembly of the barn owl (Tyto alba alba)

Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda

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