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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

Versioning


No version available

Documentation


Publication for PhyloPhlAn

PhyloPhlAn citations

 (63)
library_books

Phylogeny Trumps Chemotaxonomy: A Case Study Involving Turicella otitidis

2018
Front Microbiol
PMCID: 5936774
PMID: 29760685
DOI: 10.3389/fmicb.2018.00834

[…] od phylogenetic tree was inferred using RAxML version 8.2.8 () with the GTRGAMMA model and 100 bootstrap replications (). Another core-gene based genome-wide phylogenetic analysis was performed using PhyloPhlAn () based on CDS sequences of each genome downloaded in the previous step. The FastTree2 software implemented in this software was used to infer an approximated maximum-likelihood tree (; ). […]

library_books

Evolutionary novelty in gravity sensing through horizontal gene transfer and high order protein assembly

2018
PLoS Biol
PMCID: 5915273
PMID: 29689046
DOI: 10.1371/journal.pbio.2004920

[…] s 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 se […]

library_books

Genome centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion

2018
Biotechnol Biofuels
PMCID: 5911951
PMID: 29713376
DOI: 10.1186/s13068-018-1121-0

[…] genome-wide Average Nucleotide Identity (gANI) of the PGs against their neighboring reference genome was calculated using the JGI ANI calculator [] (Additional file ). The phylogenetic tree based on PhyloPhlAn results was drawn with GGTREE []. The metabolism of each PG was manually curated using KEGG annotations and annotations from the other databases mentioned above as required. […]

library_books

Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage specific evolution

2018
PMCID: 5955933
PMID: 29581530
DOI: 10.1038/s41396-018-0098-9

[…] oncatenated alignment of amino-acid sequences of marker genes identified by CheckM [] (Supplementary Figure ). The exact position of the Magnetococcales in two genomic trees is not consistent: in the PhyloPhlAn tree the Magnetococcales represents a sister clade to the classes of Betaproteobacteria, Gammaproteobacteria, Zetaproteobacteria, and “Candidatus Muproteobacteria” (Fig. ), while in the Che […]

call_split

Complete Genome Sequence of Loktanella vestfoldensis Strain SMR4r, a Novel Strain Isolated from a Culture of the Chain Forming Diatom Skeletonema marinoi

2018
Genome Announc
PMCID: 5864940
PMID: 29567748
DOI: 10.1128/genomeA.01558-17
call_split See protocol

[…] r’s 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 it to be a […]

library_books

On the Road to Strain Resolved Comparative Metagenomics

2018
mSystems
PMCID: 5850074
PMID: 29556534
DOI: 10.1128/mSystems.00190-17

[…] nts) 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 strain-leve […]

Citations

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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.