PhyloPhlAn protocols

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PhyloPhlAn specifications

Information


Unique identifier OMICS_01525
Name PhyloPhlAn
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for PhyloPhlAn

PhyloPhlAn in pipelines

 (17)
2018
PMCID: 5756336
PMID: 29304850
DOI: 10.1186/s40168-017-0392-1

[…] of retrieved genome bins (gbs) was carried out in prodege []. bonafide gbs were uploaded to rast [] for annotation. all gbs were checked for completeness and contamination using checkm v1.0.5 []., phylophlan v0.99 [] was used to reconstruct the phylogenetic tree of all gbs based on the protein prediction results from prodigal v2.6 []. additionally, we used blast [] to compare the 16s rrna gene […]

2018
PMCID: 5794932
PMID: 29437085
DOI: 10.1128/genomeA.00009-18

[…] 1.11 (), which identified 4,064, 2,649, and 2,877 coding sequences for the pseudomonas, flavobacterium, and sediminibacterium genomes, respectively. high-resolution phylogenetic profiling using phylophlan () and sequence similarity analysis using pyani (version 0.2.6; option “-m anib”) both confirmed that the three genomes belong to new species when using a sequence identity cutoff of 95%., […]

2018
PMCID: 5835047
PMID: 29535698
DOI: 10.3389/fmicb.2018.00333

[…] under this study are submitted in ncbi genbank and are summarized into table ., phylogenetic analysis of the isolates was carried out by constructing a tree based on 400 universal protein by phylophlan version 0.99 (segata et al., ) and was represented by interactive tree of life (itol) version 3 (letunic and bork, ). for genome similarity assessment, blast-based average nucleotide […]

2018
PMCID: 5835065
PMID: 29535685
DOI: 10.3389/fmicb.2018.00280

[…] in our samples were retained for phylogenetic calculations. for the genome tree, all complete and draft genomes of aob and nob were obtained from ncbi. the phylogenetic analysis was performed using phylophlan () with default parameters., the concentrations of nh4+ were determined using a colorimetric assay () with a spectrophotometer (spectramax m2, molecular devices, united states), while no2- […]

2017
PMCID: 5366915
PMID: 28345639
DOI: 10.1038/srep45258

[…] and mismatch correction (correction of mismatches and short indels in the assembly)., we first verified that all the genomes had a consistent number of universal marker genes as defined by phylophlan. with the exception of m. leprae which is known to be a species that underwent massive genomic reduction, the other genomes comprise an average 318 of the 400 universal markers and none […]


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PhyloPhlAn in publications

 (54)
PMCID: 5915273
PMID: 29689046
DOI: 10.1371/journal.pbio.2004920

[…] multiple strains from the same species, was pruned to retain 1 strain per species whose annotated genome is available in the ncbi reference sequence database (refseq, ftp.ncbi.nlm.nih.gov/refseq/). phylophlan [] was used to insert additional octin-possessing species that are not present in the original tree (). all other species trees (, and figs) were constructed from 400 conserved protein […]

PMCID: 5911951
PMID: 29713376
DOI: 10.1186/s13068-018-1121-0

[…] was obtained by averaging coverages of all contigs of that pg and dividing by the total number of reads in the metagenome. phylogenetic analysis of the reconstructed pgs was carried out using phylophlan [] and the online tool miga []. phylophlan uses four hundred conserved proteins from more than 3700 finished and draft microbial genomes for the construction of high-resolution […]

PMCID: 5955933
PMID: 29581530
DOI: 10.1038/s41396-018-0098-9

[…] phylogeny of genomes was constructed using raxml v8.2.8 [] (-m protgammavt -f a -x 12345 -k -p 12345 -n 100) with a concatenated alignment of the conserved ubiquitous proteins identified with phylophlan [] (fig.  and supplementary figure ). the vt+g model was used as determined by prottest 3.4 []. the genomic tree was rooted with genomes from the domain archaea (methanobrevibacter […]

PMCID: 5864940
PMID: 29567748
DOI: 10.1128/genomeA.01558-17

[…] two identical 16s rrna sequences have 99.8% identity with the three 16s sequences of l. vestfoldensis strain dsm 16212t (genbank accession number nz_arnl00000000). a phylotaxonomic analysis using phylophlan version 0.99 (), comparing strain smr4r to all whole-genome-sequenced rhodobacteraceae strains on ncbi’s refseq site (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/), showed […]

PMCID: 5850074
PMID: 29556534
DOI: 10.1128/mSystems.00190-17

[…] should be performed by relying only on very-high-quality metagenomically assembled bins and by contextualizing them through phylogenetic rather than taxonomic approaches. our new developments of phylophlan () are going in this direction, but metagenomic characterization of unknown genomes in the human microbiome remains an open challenge that is necessary to obtain a comprehensive […]


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PhyloPhlAn institution(s)
Biostatistics Department, Harvard School of Public Health, Boston, MA, USA

PhyloPhlAn review

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nick_youngblut

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Desktop
It is not available via conda. It requires usearch (and vsearch cannot just be substituted). Also, it requires running the phylophlan.py within the same directory *and* all of your files MUST be in the ./input/ directory within the main directory. In other words, phylophlan is a pain to setup and use.