References

10.1126/science.1208344

10.1126/science.1208344 · External reference

10.2337/dc14-0769

10.2337/dc14-0769 · External reference

10.1038/nm.3145

10.1038/nm.3145 · External reference

Gut microbiota and cardiovascular disease

10.1161/circresaha.120.316242 · 2020 · External reference

Gut microbiome alterations in Alzheimer's disease

2017 · External reference

10.1038/nrc3610

10.1038/nrc3610 · External reference

Improved metagenomic analysis with kraken 2

2019 · External reference

10.1111/j.1463-6409.1997.tb00423.x

10.1111/j.1463-6409.1997.tb00423.x · External reference

Phylogenetic analysis

2001 · External reference

10.1016/b978-0-12-407863-5.00019-8

10.1016/b978-0-12-407863-5.00019-8 · External reference

Metagenomic analysis using phylogenetic placement—a review of the first decade

10.3389/fbinf.2022.871393 · 2022 · External reference

10.1038/nbt.4229

10.1038/nbt.4229 · External reference

A higher level classification of all living organisms

10.1371/journal.pone.0119248 · 2015 · External reference

Unresolved reference

2019 · External reference

A phylogenetic transform enhances analysis of compositional microbiota data

10.7554/elife.21887 · 2017 · External reference

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

10.7717/peerj.2969 · 2017 · External reference

10.1111/biom.13335

10.1111/biom.13335 · External reference

Tree-aggregated predictive modeling of microbiome data

10.1038/s41598-021-93645-3 · 2021 · External reference

10.1093/jrsssc/qlac002

10.1093/jrsssc/qlac002 · External reference

Unresolved reference

External reference

Some distance properties of latent root and vector methods used in multivariate analysis

10.1093/biomet/53.3-4.325 · 1966 · External reference

10.1093/bioinformatics/btx311

10.1093/bioinformatics/btx311 · External reference

10.1109/bibm.2018.8621382

10.1109/bibm.2018.8621382 · 2018 · External reference

Microbiomes in light of traits: a phylogenetic perspective

10.1126/science.aac9323 · 2015 · External reference

A new view of the tree of life

2016 · External reference

10.1128/aem.71.12.8228-8235.2005

10.1128/aem.71.12.8228-8235.2005 · External reference

Qiita: rapid, web-enabled microbiome meta-analysis

10.1038/s41592-018-0141-9 · 2018 · External reference

Mg-rast, a metagenomics service for analysis of microbial community structure and function

2016 · External reference

The sequence read archive

2010 · External reference

Bioinformatics detection of alternative splicing

2008 · External reference

10.1126/science.1170995

10.1126/science.1170995 · External reference

Whole genome assembly from 454 sequencing output via modified dna graph concept

10.1016/j.compbiolchem.2009.04.005 · 2009 · External reference

10.1038/nbt.3893

10.1038/nbt.3893 · External reference

10.1016/0022-2836(70)90057-4

10.1016/0022-2836(70)90057-4 · External reference

Rfam: an rna family database

10.1093/nar/gkg006 · 2003 · External reference

Muscle: multiple sequence alignment with high accuracy and high throughput

10.1093/nar/gkh340 · 2004 · External reference

Unresolved reference

External reference

Identification of common molecular subsequences

10.1016/0022-2836(81)90087-5 · 1981 · External reference

Mafft: a novel method for rapid multiple sequence alignment based on fast Fourier transform

10.1093/nar/gkf436 · 2002 · External reference

Mafft online service: multiple sequence alignment, interactive sequence choice and visualization

10.1093/bib/bbx108 · 2019 · External reference

Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega

10.1038/msb.2011.75 · 2011 · External reference

10.1093/bioinformatics/btu439

10.1093/bioinformatics/btu439 · External reference

Fast gapped-read alignment with bowtie 2

10.1038/nmeth.1923 · 2012 · External reference

Hisat: a fast spliced aligner with low memory requirements

10.1038/nmeth.3317 · 2015 · External reference

Minimap2: pairwise alignment for nucleotide sequences

10.1093/bioinformatics/bty191 · 2018 · External reference

The neighbor-joining method: a new method for reconstructing phylogenetic trees

1987 · External reference

10.1007/bf01734359

10.1007/bf01734359 · External reference

10.1007/bf02338839

10.1007/bf02338839 · External reference

Bayesian phylogenetic inference using dna sequences: a Markov chain Monte Carlo method

10.1093/oxfordjournals.molbev.a025811 · 1997 · External reference

Fasttree 2–approximately maximum-likelihood trees for large alignments

10.1371/journal.pone.0009490 · 2010 · External reference

Raxml-vi-hpc: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

10.1093/bioinformatics/btl446 · 2006 · External reference

Iq-tree: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies

10.1093/molbev/msu300 · 2015 · External reference

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood

10.1080/10635150390235520 · 2003 · External reference

Beast: Bayesian evolutionary analysis by sampling trees

10.1186/1471-2148-7-214 · 2007 · External reference

Phylobayes 3: a bayesian software package for phylogenetic reconstruction and molecular dating

10.1093/bioinformatics/btp368 · 2009 · External reference

Mrbayes 3: Bayesian phylogenetic inference under mixed models

10.1093/bioinformatics/btg180 · 2003 · External reference

Unresolved reference

2012 · External reference

10.1038/s41587-019-0209-9

10.1038/s41587-019-0209-9 · External reference

Lotus2: an ultrafast and highly accurate tool for amplicon sequencing analysis

10.1186/s40168-022-01365-1 · 2022 · External reference

10.1007/s12551-021-00865-y

10.1007/s12551-021-00865-y · External reference

Phylogeny-aware analysis of metagenome community ecology based on matched reference genomes while bypassing taxonomy

2022 · External reference

Defining operational taxonomic units using dna barcode data

10.1098/rstb.2005.1725 · 2005 · External reference

10.1073/pnas.0605127103

10.1073/pnas.0605127103 · External reference

A brief overview of the concepts, methods and computational tools used in phylogenetic tree construction and gene prediction

2019 · External reference

10.1038/nmeth.3869

10.1038/nmeth.3869 · External reference

10.1093/molbev/msp077

10.1093/molbev/msp077 · External reference

phyloseq: an r package for reproducible interactive analysis and graphics of microbiome census data

10.1371/journal.pone.0061217 · 2013 · External reference

10.1017/cbo9780511819049.007

10.1017/cbo9780511819049.007 · 2009 · External reference

Multiple upgma and neighbor-joining trees and the performance of some computer packages

10.1093/oxfordjournals.molbev.a025590 · 1996 · External reference

10.1093/molbev/msab120

10.1093/molbev/msab120 · External reference

Tnt, a free program for phylogenetic analysis

10.1111/j.1096-0031.2008.00217.x · 2008 · External reference

10.1038/s41587-023-01688-w

10.1038/s41587-023-01688-w · External reference

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains bacteria and archaea

10.1038/s41467-019-13443-4 · 2019 · External reference

Kraken: ultrafast metagenomic sequence classification using exact alignments

2014 · External reference

Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of motus across various environments

10.1186/s40168-022-01410-z · 2022 · External reference

A dna-based registry for all animal species: the barcode index number (bin) system

10.1371/journal.pone.0066213 · 2013 · External reference

10.1038/nbt.2579

10.1038/nbt.2579 · External reference

10.1101/gr.142315.112

10.1101/gr.142315.112 · External reference

10.1038/nmeth.2693

10.1038/nmeth.2693 · External reference

Microbial abundance, activity and population genomic profiling with motus2

10.1038/s41467-019-08844-4 · 2019 · External reference

10.1016/j.cell.2019.01.001

10.1016/j.cell.2019.01.001 · External reference

Unresolved reference

External reference

10.1038/s41592-018-0176-y

10.1038/s41592-018-0176-y · External reference

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using phylophlan 3.0

10.1038/s41467-020-16366-7 · 2020 · External reference

Astral-iii: polynomial time species tree reconstruction from partially resolved gene trees

10.1186/s12859-018-2129-y · 2018 · External reference

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in r

10.1093/bioinformatics/bty633 · 2019 · External reference

10.1038/ismej.2011.139

10.1038/ismej.2011.139 · External reference

High throughput ani analysis of 90k prokaryotic genomes reveals clear species boundaries

10.1038/s41467-018-07641-9 · 2018 · External reference

Greengenes2 unifies microbial data in a single reference tree

2023 · External reference

Variance adjusted weighted unifrac: a powerful beta diversity measure for comparing communities based on phylogeny

10.1186/1471-2105-12-118 · 2011 · External reference

10.1093/bioinformatics/bts342

10.1093/bioinformatics/bts342 · External reference

10.1111/jgh.15503

10.1111/jgh.15503 · External reference

Explainable ai reveals changes in skin microbiome composition linked to phenotypic differences

10.1038/s41598-021-83922-6 · 2021 · External reference

10.1093/sysbio/syac031

10.1093/sysbio/syac031 · External reference

Scaling depp phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach

10.1093/bioinformatics/btae361 · 2024 · External reference

Structure-based protein function prediction using graph convolutional networks

10.1038/s41467-021-23303-9 · 2021 · External reference

10.1038/s41588-018-0295-5

10.1038/s41588-018-0295-5 · External reference

A novel deep learning method for predictive modeling of microbiome data

10.1093/bib/bbaa073 · 2021 · External reference