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#1Advanced Tutorial - IQ-TREE
... aware data structure for phylogenomic inference from supermatrices. ... iqtree -s example.phy -p example.partitions -m GTR+I+G # for ...
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#2Terrace Aware Phylogenomic Inference from Supermatrices
Here, we propose a phylogenetic terrace aware (PTA) data structure for efficient supermatrix based tree inference under partition models. PTA ...
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#3Evaluating Fast Maximum Likelihood ... - Oxford Academic
2014), and the two data sets correspond to the same supermatrix. ... first to the fourth best (IQTREE-10, RAxML-10, IQTREE, and PhyML-10).
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#4IQ-TREE - Workshop on Molecular Evolution
Supermatrix. Gene 1. Gene 2 …… Gene 1,000. Gene Concordance Factor (gCF):. How often a branch in species tree is found among gene trees? 0% ≤ gCF ≤ 100% ...
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#5Phylogenomic inference with IQ-TREE - Evolution and ...
Rate model Explanation. +I. Some sites are invariable (zero rate), e.g. due to selective force. +G. Site rates follow a Gamma distribution.
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#6IQ-Tree - GitHub
... for efficient phylogenomic software by maximum likelihood http://www.iqtree.org. ... aware data structure for phylogenomic inference from supermatrices.
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#7IQ-TREE 2: New Models and Efficient ... - ANU Open Research
Chernomor O, von Haeseler A, Minh BQ. 2016. Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol. 65(6):997–1008. Crotty ...
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#8(PDF) W-IQ-TREE: a fast online phylogenetic tool for ...
W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary models ...
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#9An investigation of irreproducibility in maximum likelihood ...
... phylogenies inferred twice from the same supermatrix are reproducible. ... iqtree–runs 1 -nt 10 -st DNA -seed 369284957 -me 0.0001 -s ...
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#10Part 4: Multigene phylogenetics
For this reason, merging each individual datasets into a supermatrix is essential. ... iqtree -p partition.nex -m WAG+I+G4 [-T AUTO -B 1000].
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#11Terrace Aware Data Structure for Phylogenomic Inference ...
supermatrices, missing data may hamper the tree search algorithms due to the existence of phylogenetic (partial) terraces.
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#12Supermatrix alignment has varying length -> error in tree build
I'm attempting to use PhyloPhlan to build a tree from some MAGs, but obtaining an error in tree building (with IQTREE): ERROR: Sequence ...
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#13Paralogs and Off-Target Sequences Improve Phylogenetic ...
exon.codon.noparalogs*, Coding sequences, without paralogs, Supermatrix, RAxML, ... based on IQtree gene trees employing the best model for each gene.
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#14W-IQ-TREE: a fast online phylogenetic tool for maximum ...
W-IQ-TREE performs fast model selection, partition scheme finding, efficient tree reconstruction, ultrafast bootstrapping, branch tests, and tree topology tests ...
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#15PhyloFisher: A phylogenomic package for resolving eukaryotic ...
Attempts to minimize phylogenetic saturation by recoding input supermatrix into the. 4-character state scheme of SR4, based on amino acid ...
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#16Ultra‐Conserved Elements and morphology reciprocally ...
Analyses of 538 Ultra‐Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ASTRID) resulted in ...
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#17Terrace aware data structure for phylogenomic inference from ...
In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of ...
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#18Data for supermatrix phylogeny of ... - Research Data Australia
DNA sequence data alignments, partitioning information and resulting phylogenetic trees for study of evolutionary relationships of the groundsel tribe ( ...
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#19Phylogenetics | Caenorhabditis Genomes Project
This tree was inferred using IQ-TREE using a supermatrix containing 982 single-copy orthologues (BUSCO nematode genes). It was rooted on two outgroup taxa, ...
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#20phylogenetic conflict and systematic error - University of ...
When analyzing supermatrix H, we selected. 360 the full set of COGs to perform the species tree analysis, as this dataset had already a low. 361 proportion of ...
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#21Phylogenomic analyses of 142 prokaryotic genera | Zenodo
Name Size Blautia.tar; md5:b897d8910fa9623b2a8dcbbcbc48cf2d 76.7 MB Download Devosia.tar; md5:012ccad1cc6b004301945ddd4ed84ab1 104.8 MB Download Dickeya.tar; md5:40f89254c727f24b1e681dd203dc5198 53.9 MB Download
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#22Rémi Allio on Twitter: "Phylogenetic inferences were ...
Phylogenetic inferences were performed with both supermatrix approaches (Maximum Likelihood with IQ-TREE and Bayesian inferences with ...
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#23Phylomitogenomic analyses on collembolan higher taxa with ...
tion models on supermatrices A1, A2 and A3 were selected using ... tion, we also inferred trees from supermatrix A1 under the codon model ...
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#24UFBoot2: Improving the Ultrafast Bootstrap Approximation
freely available at http://www.iqtree.org. ... inferred from a supermatrix of mitochondrial and nuclear DNA. Mol. Phylogenet. Evol.
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#25超保守元素和形态学相互阐明了Chalcididae（膜翅目 - X-MOL
Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ...
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#26Data for supermatrix phylogeny of the Senecioneae
DNA sequence data alignments, partitioning information and resulting phylogenetic trees for study of evolutionary relationships of the groundsel ...
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#27Olga Chernomor - Google Scholar
Terrace aware data structure for phylogenomic inference from supermatrices. O Chernomor, A Von Haeseler, BQ Minh. Systematic biology 65 (6), 997-1008, 2016.
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#28Evidence from multiple gene phylogenies and extrolites profiles
... aBayes and UFML bootstrap support for IQTREE; Rapid ML bootstrap support ... Terrace aware data structure for phylogenomic inference from supermatrices.
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#29IQ-TREE 2: New Models and Efficient Methods for ... - Meta.org
IQ-TREE (http://www.iqtree.org, last accessed February 6, ... Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices.
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#30Genome sequences identify three families of Coleoptera as ...
filtered data, supermatrix contains all genes for all taxa generated by AliStat. Shared site coverage is shown from dark blue (low) to white (high) .
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#31Recent Progress on Methods for Estimating and Updating ...
IQTree. RAxML. GTM. Figure 3: We compare standard maximum likelihood methods ... “supermatrix” and estimates a tree on the supermatrix, ...
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#32A Phylogenomic Supertree of Birds | HTML - MDPI
The supermatrix approach has obvious appeal since it simply involves combining sequence data and conducting standard phylogenetic analyses. However, supermatrix ...
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#33Evaluating Fast Maximum Likelihood ... - Vanderbilt University
approach, the species tree is estimated from the supermatrix ... (IQTREE-10, RAxML-10, IQTREE, and PhyML-10). Among basic strategies, RAxML performed better ...
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#34Neoproterozoic origin and multiple transitions to macroscopic ...
phylogenetic methods, including supermatrix and the coalescence- ... supermatrix analyses were performed using IQtree with two settings: 1) ...
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#35Taxon sampling to address an ancient rapid radiation - Scinapse
Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera). Published on Apr 1, 2018in Systematic ...
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#36Cai_et_al_MPE.pdf - University of Bristol Research Portal
Among the eleven amino-acid supermatrices they generated, their focal analyses were. 107 principally based upon the full dataset (Supermatrix A: 14 taxa, ...
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#37Best method for phylogeny on bacterial genes - Biostars
I have installed raxml, iqtree and megax, and I can work with all of them ... then to use the super matrix as input for a phylogenetic tool.
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#38Olga Chernomor - Center for Integrative Bioinformatics Vienna
(2016) Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices. ... IQ-TREE - http://www.cibiv.at/software/iqtree/about/ ...
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#39Evaluating fast maximum likelihood-based ... - Figshare
In contrast, PhyML often failed to complete runs on supermatrices, whereas FastTree was the fastest of all programs in both types of ...
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#40Ultra-Conserved Elements and morphology reciprocally ...
Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix. 34. (RAxML and IQTREE) and gene-tree reconciliation approaches (ASTRAL, ...
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#41Iq Tree
... and versatile phylogenomic software by maximum likelihood http://www.iqtree.org ... aware data structure for phylogenomic inference from supermatrices.
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#42Mitochondrial genome of the freshwater annelid Manayunkia ...
supermatrix was conducted with IQTree (Nguyen et al. 2015). Substitution models and partitions were determined automatically.
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#43Genome-scale data resolve ancestral rock-inhabiting lifestyle ...
Maximum likelihood (ML) phylogenetic inferences from the supermatrix, as well as the single-locus inferences, were produced with IQTree ...
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#44BUSCO_phylogenomics from SolayMane - Github Help
Works directly from BUSCO output and can be used for supermatrix or supertree/coalescent methods. ... muscle , trimal and iqtree should be in $PATH ...
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#45Molecular Phylogenetics and Evolution - Mendeley Data
... and concatenated supermatrix) and gene trees used for data exploration. ... and a maximum likelihood phylogram obtained with IQTREE in newick format.
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#46Evolutionary history and divergence times of Odonata ...
and all three codon positions comprised of 824,783 (supermatrix B) and ... 2020a) (Figure S2) as implemented in IQTREE version 2.0-rc2 (Minh.
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#47Levy_RPSDOWN_thesis.pdf - UCL Discovery
3.3.2 OMA Variants Produces Large Supermatrices with Few Gaps . . . 76 ... Foulds distance between IQTREE and FastTree, PAUP,.
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#48Phylogenomics of the Caddisfly Genus Smicridea, With A ...
I used maximum likelihood, as implemented in the software IQ-TREE, to analyze the sequence supermatrix as well as the "summary" method ASTRAL-III, ...
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#49GET_PHYLOMARKERS, a Software Package to ... - Frontiers
... were concatenated into a supermatrix of 38,415 aligned residues, ... to the species tree inferred from the corresponding supermatrix.
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#50Molecular Phylogeny and Historical Biogeography of the ...
The concatenated supermatrix was analyzed with maximum likelihood (ML) inference using IQtree 1.4.2 [17]. To assess nodal support, we performed ...
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#51An updated phylogeny of the Alphaproteobacteria reveals that ...
All this was done before concatenating the single-gene alignments into a supermatrix with SequenceMatrix v 1.8 (Vaidya et al., 2011).
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#52Untangling the early diversification of eukaryotes - Journals
A 234-taxa, 263-gene (234/263) supermatrix was then constructed to infer an initial maximum-likelihood (ML) tree with IQ-TREE v. 1.3.0 [30] under the LG þ G ...
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#53OMA standalone: orthology inference among public and ...
The construction of large phylogenomic supermatrices has been the method of choice ... (B) The resulting supermatrix has most sites for OMA, ...
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#54first phylogenomic reconstruction of the nudibranch
IQTree was implemented using the supermatrix and partition output from PhyloPyPruner. Amino acid datatype (AA) was selected using the -st option.
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#55Taxonomic sampling and rare genomic changes overcome ...
Keywords: arachnids, ohnologs, supermatrix, species tree reconciliation, microRNA. ScholarOne, 375 Greenbrier Drive, Charlottesville, VA, ...
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#56Novel, exotic Wolbachia genomes - Michael Gerth
Figure 3: Maximum likelihood phylogeny of Wolbachia supergroups. Tree is based on partitioned amino acid supermatrix analysis with IQTREE (119 ...
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#57Pangenomic and phylogenomic analyses of pIncC plasmids ...
... 4.2.1.3 The top_N_markers_geNperc directory holds the supermatrix ... launching 10 independent iqtree searches on # all available cores ...
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#58Supertree Construction: Opportunities and Challenges
[118], PhyML [56], IQTree [87], and FastTree-2 [97]. ... palms (arecaceae) with comparisons of supertree and supermatrix approaches.
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#59iqtree partitionfinder - окуасп
The phylogeny is inferred by IQTREE and RAxML based on a concatenated supermatrix containing 121 genes (14 mitochondrial and 107 nuclear) ...
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#60The Brown Lab
Supermatrices are constructed from these bins of orthologs. SR4_class_recoder.py: Attempts to minimize phylogenetic saturation by recoding input supermatrix ...
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#61Identification and Functional Characterization of Novel ...
Cleaned sequences recovered from the collection of OGTs were concatenated in a supermatrix partitioned by locus, using the script geneStitcher.py [54].
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#62Microbial Taxonomy, Phylogeny and Biodiversity
majority rule consensus (mjrc) tree of top-scoring gene-trees, or as the tree estimated from the supermatrices of concatenated alignments.
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#63Advances in Genetics - 第 192 頁 - Google 圖書結果
Trimmed alignments were then concatenated, resulting in a supermatrix of 44,739 amino acid residues. Maximum-likelihood analysis was performed using IQ-TREE ...
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#64Genomics and Effectomics of the Crop Killer Xanthomonas
... by FASconCAT yielding a nucleotide supermatrix (Kück and Meusemann, 2010). ... analysis for phylogeny construction was performed using IQTree v.1.1.5 ...
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#65Bioinformatics and Phylogenetics: Seminal Contributions of ...
Thus, taking terraces into account allows for memory savings that are proportional to the fraction of missing data in the supermatrix.
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#66Phylogenomics: A Primer - Google 圖書結果
... 297, 299 IQtree, partitions in, 305 NEXUS, partitions in, 302–305 PAML files, ... 312–313 supertrees/supermatrices, 313–316 PHYLogeny Inference Program ...
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#67Microbial Drivers of Sociality – from Multicellularity to ...
... a maximum-likelihood (ML) approach with IQTREE v1.5.4 create the ortholog ... sequence alignments (MSAs) were concatenated into a supermatrix (see also ...
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#68Bioinformatics of Genome Regulation and Systems Biology
This approach results in alignment filtering at the supermatrix construction step. The “circular” contigs starting and ending with the same k-mer. obtained ...
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#69Quantitave Analysis of Phylogenetic Quasi-Terraces
These large matrices (also called supermatrix or phylogenomic data set) are ... iqtree -s [name].phy -spp [name].partition -te [name].linked.bestTree -z.
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