PhyloPhlAn pipeline

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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Documentation


Publication for PhyloPhlAn

PhyloPhlAn IN pipelines

 (3)
2017
PMCID: 5278652
PMID: 28138345
DOI: 10.7150/jgen.17863

[…] v0.35, spades v3.6.2, sspace v3.0 and gapfiller v1.10, respectively 6-9. genomic relatedness among different strains was inferred based on average nucleotide identity (ani) using jspecies v1.2.1 10. phylophlan v0.99 was subsequently used to infer the evolutionary relationship among the sequenced strains and related strains/species 11., pangenome analysis was performed with roary […]

2017
PMCID: 5701469
PMID: 29167244
DOI: 10.1128/genomeA.01294-17

[…] completeness with no indication of contamination or strain heterogeneity), and scaffolded through sspace (7)., the assembled draft genome was confirmed to belong to the t. bourrellyi species by phylophlan analysis (8) and blastn searches of the 16s and rbclx genes, which were 98.7% and 100% identical, respectively, to previously reported t. bourrellyi genes (3). the genome is 5.08 mb […]

2016
PMCID: 4926282
PMID: 27353502
DOI: 10.1038/srep28810

[…] t from the maximum overlap parameter, which was set to 150. gene finding and annotation and binning was performed following the strategy developed by campanaro et al.19. taxonomy was determined using phylophlan42 and further refined using phylopythia software43. kegg functional analysis was refined using ghostkoala (http://www.kegg.jp/ghostkoala/). reads were aligned on scaffolds larger than 500 b […]

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.