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#1Rooting phylogenies - IQ-TREE
Inferring unrooted tree with outgroup. We first demonstrate the outgroup approach to root the Bovidae family of five sampled species (Yak, Cow, ...
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#2How to specify several outgroups in IQ-TREE? - ResearchGate
I also have a try to specify a comma-separated taxa name of outgroups ... It really seems unlikely that IQtree can define just one sequence as an outgroup.
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#3-o outgroup option causes error - Google Groups
I believe the taxon I am assigning as outgroup is not present in all ... scripts/IQ-Tree1.6.beta4/bin/iqtree -nt $cpus -st AA -ninit 10 -bb 1500 -pre ...
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#4IQ-Tree-Teaching - Research Computing Center Wiki
module load IQ-TREE/1.6.12-foss-2019b iqtree -h IQ-TREE multicore ... user tree (no tree search performed) -o <outgroup_taxon> Outgroup ...
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#5Maximum-Likelihood Phylogenetic Inference - tutorials ...
IQTREE. Here, you'll see that IQ-TREE has apparently automatically performed a test ... To correct the rooting of the phylogeny, we can specify an outgroup.
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#6add an outgroup to an unrooted tree - Biostars
Hi, I am quite new to phylogenetic analysis. Please bare with me if question does not make sense. I am using IQtree to analyse som… Rooting ...
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#7man iqtree (1): efficient phylogenetic software by maximum ...
man iqtree (1): IQ-TREE version 1.4.2 for Linux 64-bit built Jun 29 2016 Copyright ... -o <outgroup_taxon>: Outgroup taxon name for writing .treefile ...
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#8Fig. 5 - BMC Genomics
... genomes were used to infer a maximum likelihood phylogenetic tree using IQTREE. ... Since there was no outgroup included in the tree, FigTree's midpoint ...
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#9A method for achieving complete microbial genomes ... - PLOS
We specified the Margulisbacteria as the outgroup when creating the tree using IQ-TREE with ultrafast bootstrap [53]. The ribosomal operon structure is ...
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#10Detailed command line documentation - TreeTime
... the alignment using fasttree, iqtree, or raxml (assuming they are installed) ... to be used as outgroup or use 'oldest' to reroot to the oldest node.
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#11Outgroup, alignment and modelling improvements indicate ...
Outgroup, alignment and modelling improvements indicate that two TNFSF13-like genes existed in the vertebrate ancestor.
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#12Part 5: Testing phylogenies
iqtree -s ALIGNMENT_FILE --trees TREES_FILE --test-weight --test-au --test 10000 -m ... You will be asked to select the outgroup for rooting the tree.
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#13Rooting the Animal Tree of Life - Oxford Academic
(C) The animals and their outgroup choice, showing the three progressively more inclusive clades Choanozoa, Holozoa, and Opisthokonta. (D) A ...
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#14nQMaker: estimating time non-reversible amino acid ... - X-MOL
... is that they do not allow inference of rooted trees without outgroups. ... feature in the IQ-TREE software (http://www.iqtree.org), ...
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#15iqtree-omp(1) - Debian Manpages
iqtree -omp - efficient phylogenetic software by maximum likelihood (multiprocessor ... -o <outgroup_taxon>: Outgroup taxon name for writing .treefile ...
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#16Tree rooting with PhyloPhlan - The bioBakery help forum
A genus of archaebacteria is being used as an outgroup to root my tree. ... or IQ-TREE (http://www.iqtree.org/doc/iqtree-doc.pdf) there are ...
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#17nQMaker: estimating time non-reversible amino acid ... - bioRxiv
(http://www.iqtree.org), allowing users to estimate ... Non-reversible models remove the need for an outgroup because the root position.
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#18treeio.pdf - Bioconductor
read.iqtree . ... a vector of mode numeric or character specifying the new outgroup node node to reroot edgelabel.
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#19Ebola virus phylogenetic analysis protocol - Artic Network
The -pre new_genomes.iqtree option defines what the output files will be called. ... gotree reroot outgroup -i new_genomes.iqtree.treefile ...
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#20iqtree-omp - efficient phylogenetic software ... - Ubuntu Manpage
... search performed) -o <outgroup_taxon> Outgroup taxon name for writing .treefile -pre <PREFIX> Using <PREFIX> for output files (default: aln/partition) ...
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#21基于ML法重建系统发育树-IQ-TREE篇 - 360doc个人图书馆
该软件的具体功能详见官方网站介绍（http://www.iqtree.org/），本文不再 ... 在模型参数之后，添加一个-o 参数用以指定某一条序列为outgroup，如：-o ...
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#22Phylogenetic Tree with Reference Sequences - User Support
... generating the ML tree (with bootstraps) and rooting it with the outgroup. ... and use either the iqtree or the iqtree-ultrafast-bootstrap approach.
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#23The complete chloroplast genome sequence of Asplenium ...
Phylogenetic analysis based on 21 representative chloroplast genomes of the suborder Aspleniineae (and one outgroup) indicates that ...
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#24Running ClusTRace | ClusTRace | University of Helsinki
--ufboot, false, Run iqtree with ultrafast bootstrap and create consensus ... If --outgroup is a directory the pipeline will look for an ...
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#25IQ TREE Versions - Open Source Agenda
Moreover, the outgroup will now be kept in the time tree by default. Bugfixes: Crash with -bnni option and GHOST model (reported by Miles Zhang and thanks ...
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#26Tree manipulation - WoL
root_by_outgroup.py input.nwk outgroup.list > output.nwk. This script allows incomplete taxon list: the tree may contain less taxa (e.g., a subsampled tree) ...
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#27Using target sequence capture to improve the phylogenetic ...
additional 200 kbp of flanking noncoding sequences for each of 77 hebe and two outgroup species. When comparing coding, noncoding, and combined data sets, we ...
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#28Phylogenetic reconstruction of diatoms using a seven-gene ...
Abstract: Medlin tested multiple outgroups with 18S rRNA dataset and found that haptophytes, ciliates, prasinophytes, and chlorophytes recovered monophyletic ...
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#29IQ TREE 2.1.3 - CQLS Software Update List
which iqtree2 /local/cluster/bin/iqtree2 $ iqtree2 --version IQ-TREE multicore version 2.1.3 COVID-edition for Linux 64-bit built Apr 21 ...
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#30Molecular Phylogenetics and Evolution - NSF PAR
Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants. Marek L. Borowieca,b,e,⁎, Christian Rabelingb, Seán G. Bradyc, ...
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#31A Robust Phylogenomic Time Tree for Biotechnologically and ...
Assessment of individual gene set completeness showed that most of the 93 genomes (81 in the ingroup and 12 in the outgroup) used in our ...
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#32Previous changeset 0:05ee0a74faef (2017-11-15)
iqtree.xml ... +++ b/iqtree.xml Wed Nov 15 12:45:24 2017 -0500 ... **.iqtree** file:\n+\n+**NOTE**: Tree is UNROOTED although outgroup taxon \'LngfishAu\' ...
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#33root-method: root in treeio: Base Classes and Functions for ...
phy. tree object. outgroup. a vector of mode numeric or character specifying the new outgroup. node. node to reroot. resolve.root.
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#34Compositional heterogeneity and outgroup choice influence ...
... and outgroup choice influence the internal phylogeny of the ants". ... sim-all-pos-1.fas.iqtree 38.7 kB; sim-all-pos-1.fas.log 22.7 kB ...
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#35IQ-TREE Version 2.1.2: Tutorials And Manual Phylogenomic ...
CONTENTS9.19.29.35Inferring unrooted tree with outgroup . ... IQ-TREE has been developed since 2011 and freely available at http://www.iqtree.org/ as ...
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#36Dryad Data -- A taxonomic review and revisions of ...
... CO1 sequences of all specimens used in the study as well as outgroups. ... We performed 1000 ultrafast bootstrap replicates in IQTree, ...
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#37PastML How To - Institut Pasteur
... with your favourite tool, e.g. PhyML, RAxML, FastTree, IQTree, or Beast2. Once inferred the tree must be rooted (with an outgroup or with dates, ...
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#38基於ML法重建系統發育樹-IQ-TREE篇 - 人人焦點
NC_018093_SPVG即將示例中的名稱爲NC_018093_SPVG指定爲outgroup； （2）ultrafast bootstrap approximation (UFBoot) 爲IQ-TREE引入的一個算法，適用於大 ...
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#39Standardized phylogenetic and molecular evolutionary ...
fergusonii as an outgroup (Table S1). PhaME detected 266,969 SNPs within the conserved core genome which consists of 2,159,296 aligned ...
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#40Molecular Phylogenetic Analysis of the AIG Family in ... - MDPI
outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to. ADTRP and AIG1 after two rounds of ...
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#41Phylogenetics | 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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#42Fig. 3. | Microbiology Society
... script (https://github.com/nylander/catfasta2phyml) prior to generation of the tree. Parapedobacter koreensis (FNZR00000000) was used as an outgroup.
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#43Detection of potential new SARS-CoV-2 Gamma-related ...
... construct a phylogenetic tree, we first aligned the 78 newly sequenced genomes and the reference genome as outgroup MAFFT v.7.480 [15].
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#44Phylogenetic tree and ancestral sequence reconstruction
... and closely related complete outgroup sequence(s) with MAFFT. ... RAxML amino acid substition model and branch support with IQTree.
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#45An updated phylogeny of the Alphaproteobacteria reveals that ...
Please perform an analysis including Rickettisales (but not Holosporales and Pelagibacterales) and no outgroup and see if the position of ...
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#46IQTree XSEDE REST interface - CIPRES
This interface is used from the REST API to configure IQTREE runs. ... vparam.specify_outgroup_ - (String) - Specify an outgroup (-o); no default.
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#47Diversification of giant and large eukaryotic dsDNA viruses ...
ML phylogenetic tree of the concatenated 2 largest RNAP subunits from Archaea, Eukaryotes, and NCLDVs, with Archaea serving as the outgroup. The ...
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#48Tutorial part5 - PanTools manual - Bioinformatics
pantools version Rscript --help mafft -h iqtree -h fasttree -h ... When you have a known outgroup or one of the genomes is a clear outlier in the tree, ...
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#49Supp. file 1 - European Journal of Taxonomy
Outgroup taxa were pruned off. Specimens identified by two-digit locality code in bold, four digit individual DNA code, and orographic unit (see Table 1) or ...
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#50Whole genome shotgun phylogenomics resolves the pattern ...
6,621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species. (with 32% missing data after cleaning phases).
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#51Loading phylogenetic trees into R
path/to/tipNameFile') , or tipLabels to manually specify the names of the tips (e.g. ReadTntTree(treeFile, tipLabels = c('outgroup', ...
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#52Reconstruction of protein domain evolution using single-cell ...
Finally, we included an extensive outgroup composed by holomycotans (18 taxa), apusomonads (2 taxa), breviates (3 taxa) and amoebozoans (4 ...
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#53Jiao et al. The Penium margaritaceum Genome
... were constructed using IQ-TREE (http://www.iqtree.org/) with the function of ... viride (n=1) sequences and GH7 cellulases (as outgroup), then trimmed.
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#54The Estimated Pacemaker for Great Apes Supports the ...
sequence was used as outgroup throughout the analyses. Alignments that contained non-unique sequences for any of the species were discarded, leading to a ...
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#55arbow - PyPI
conda install -c bioconda iqtree pip<3> install arbow ... [default: 5] -io, --iqtree-outgroup TEXT ID(s) of samples to be used as outgroup in IQTree.
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#56Abstract Detail - Botany 2018
... and seven outgroup species were sequenced using Illumina technology. ... trees were inferred in partitioned maximum likelihood analyses in IQTree.
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#57GRASP Ancestral Sequence Reconstruction
Cytochromes P450 are key drug metabolisers and we wish to infer a CYP2U1 ancestor. We will be using four CYP2R1 sequences as an outgroup and these four ...
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#58An Expanded Ribosomal Phylogeny of Cyanobacteria ...
... using IQtree (LG model with four gamma distributed rate categories). ... For non-recoded analyses that included bacterial outgroups for ...
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#59Error: Argument of option -a must be an integer. #128
I used iqtree for tip dating. my cmd is iqtree -s full.fasta -o outgroup --date full_date.tsv --date-root 2013-07-24 --date-tip 2020-03-26 -nt AUTO.
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#60Molecular Phylogenetics and Evolution - AntWiki
Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants. Marek L. Borowieca,b,e,⁎, Christian Rabelingb, ...
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#61Notes on the leaf insects of the genus - ZooKeys
Maximum likelihood tree of 18 Phyllium specimens from Java and Sumatra and three outgroup species. The phylogenetic tree was generated with IQ- ...
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#62root function - RDocumentation
root reroots a phylogenetic tree with respect to the specified outgroup or at the node specified in node . unroot unroots a phylogenetic tree, or returns it ...
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#63Phylogenetic tree template - arduinobastelkeller
It should be noted here that an outgroup is a lineage that falls outside the clade being studied but is closely related to that clade.
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#64Phylogenetic tree template - Himmlische Hexe
It should be noted here that an outgroup is a lineage that falls outside the clade being studied but is closely related to that clade.
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#65Working With Tree Data Structures — ETE Toolkit - analysis ...
... (duplicating) trees; Solving multifurcations; Tree Rooting; Working with branch distances. Getting distances between nodes; getting midpoint outgroup ...
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#66How to root a phylogenetic tree: outgroup, midpoint and other ...
Googling terms like "outgroup rooting" will, of course, provide several other places on the internet where people have explained how ...
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#67Innate Immunity in Aquatic Vertebrates - 第 237 頁 - Google 圖書結果
... criterion was used for model selection using IQtree's ModelFinder (77), ... Outgroup-free rooted phylogenetic analyses were performed using a relaxed ...
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#68The RAxML v8.2.X Manual
You avoid the outgroup affecting the branch lengths of the ingroup because of the way the evolutionary placement algorithm has been built.
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#69Bioinformatics and Functional Genomics - 第 290 頁 - Google 圖書結果
There are many options for the analysis type, choice of outgroup, ... UFboot are available online and for download at http://www.cibiv. at/software/iqtree.
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#70Genome Mining and Marine Microbial Natural Products
Comparative Genomic Analysis of Marine Streptomyces Genomes Kitasatospora setae KM-6054T was used as an outgroup in the further phylogenomic analysis based ...
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#71Ciliate Biodiversity and Evolution from Morphological, ...
Eight sequences of pleuronematids were selected as the outgroup. ... 2014) and IQTREE, and one Bayesian inference (BI) analysis, were carried out according ...
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#72Organelle Genetics in Plants - 第 135 頁 - Google 圖書結果
We used IQtree v1.7 and MrBayes 3.2 to perform maximum-likelihood analysis and Bayesian inference, respectively [29 ... Cladophorales was used as outgroup.
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#73Select workflow - autoMLST: Automated Multi-Locus Species ...
By default, up to 5 species are used for outgroups. Users are able to add organisms from the outgroup list to this selection or remove them.
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#74Systematics and Conservation of Neotropical Amphibians and ...
included) and includes the aromobatid Allobates femoralis as an outgroup taxon. In many cases, we include multiple representatives of a given species to ...
iqtree 在 コバにゃんチャンネル Youtube 的精選貼文
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iqtree 在 大象中醫 Youtube 的精選貼文