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GraPhlAn specifications


Unique identifier OMICS_11549
Name GraPhlAn
Alternative name Graphical Phylogenetic Analysis
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes





  • person_outline Nicola Segata

Publication for Graphical Phylogenetic Analysis

GraPhlAn citations


Profiling microbial strains in urban environments using metagenomic sequencing data

Biol Direct
PMCID: 5944035
PMID: 29743119
DOI: 10.1186/s13062-018-0211-z

[…] y the total branch length, using custom python scripts based on BioPython BaseTree [, ].The phylogenetic trees were built with RAxML [] version 8.1.15 (parameters: -p 1989 -m GTRCAT) and plotted with GraPhlAn []. Minimum Spanning Trees were drawn with PHYLOViZ 2 [] using the goeBURST Full MST algorithm []. The principal component analysis (PCA) plots were drawn with the scikit-learn package using […]


Elucidation of the bacterial communities associated with the harmful microalgae Alexandrium tamarense and Cochlodinium polykrikoides using nanopore sequencing

Sci Rep
PMCID: 5871755
PMID: 29593350
DOI: 10.1038/s41598-018-23634-6

[…] different PCR primers, virtual PCR of the database with a different number of mismatches was performed using a script from MOTHUR software called pcr.seqs.. The phylogenetic tree for visualization by GraPhlAn was generated with maximum likelihood distance,. […]


Fecal microbiota in the female prairie vole (Microtus ochrogaster)

PLoS One
PMCID: 5868765
PMID: 29579049
DOI: 10.1371/journal.pone.0190648
call_split See protocol

[…] elative abundance) and then imported into MEGAN6 to prepare phylogenetic trees []. A circular cladogram visualizing OTUs and their relative abundances at up to six taxonomic levels was constructed in GraPhlAn []. For additional diversity analyses of the overall fecal microbiota taxonomic profiles of individual and grouped animals (e.g., sibling pairs), a summed OTU table was generated combining th […]


A highly adaptive microbiome based association test for survival traits

BMC Genomics
PMCID: 5859547
PMID: 29558893
DOI: 10.1186/s12864-018-4599-8
call_split See protocol

[…] As for visual representations of discoveries, we used an existing software tool, GraPhlAn [], which is addressed later in our real data analysis. As GraPhlAn is flexibly customizable with beautiful circular representations of hierarchical taxonomic tree [], here, we do not introdu […]


Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin

Front Microbiol
PMCID: 5855357
PMID: 29593680
DOI: 10.3389/fmicb.2018.00431

[…] For both metagenomic and metatranscriptomic reads, MetaPhlAn2 and GraPhlAn software (Truong et al., ) were utilized to obtain the relative abundance of each OTU. The top 50 (relative abundance) OTUs were chosen and displayed in a dendrogram heatmap. Circular taxonom […]


Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

Nat Commun
PMCID: 5830445
PMID: 29491419
DOI: 10.1038/s41467-018-03317-6

[…] process. Initially a tree consisting of the 913 RUGs, the 410 Hungate 1000 genomes and genomes from the Uniprot results with >80% protein identity was calculated with PhyloPhlAn and visualized using GraPhlAn and FigTree. This initial tree, which relates the RUGs to their most closely related genomes, in combination with the outputs from CheckM, UniProt and Sourmash searches, allowed us to assign […]


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GraPhlAn institution(s)
Centre for Integrative Biology (CIBIO), University of Trento, Italy; Biostatistics Department, Harvard School of Public Health, USA; Broad Institute of MIT and Harvard, MA, USA
GraPhlAn funding source(s)
This work has been supported by NIH R01HG005969, NSF CAREER DBI-1053486, and W911NF-11-1-0473 and by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no PCIG13-GA-2013-618833, startup funds from the Centre for Integrative Biology (University of Trento), by MIUR “Futuro in Ricerca” E68C13000500001, by Terme di Comano, and by from Fondazione Caritro.

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