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Picante specifications


Unique identifier OMICS_06548
Name Picante
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


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Picante citations


Macroecology and macroevolution of the latitudinal diversity gradient in ants

Nat Commun
PMCID: 5934361
PMID: 29725049
DOI: 10.1038/s41467-018-04218-4
call_split See protocol

[…] ersity is presented in Supplementary Note .We calculated phylogenetic diversity (MPD) both for species grouped into latitudinal bands as well as for species occurring in each polygonal area using the picante package in R. For each species the minimum and maximum latitude of their distribution was estimated from the geographic dataset. For a given species, this was the minimum and maximum latitude […]


Exposure to toxic metals triggers unique responses from the rat gut microbiota

Sci Rep
PMCID: 5919903
PMID: 29700420
DOI: 10.1038/s41598-018-24931-w
call_split See protocol

[…] ha diversity measures were calculated using the “estimate_richness” function for OTU richness and Shannon’s Diversity, and Faith’s phylogenetic distance was calculated using the “pd” function of the “picante” R package. One-way ANOVA was used to calculate if dose significantly altered alpha diversity. The Kruskal-Wallis test was used to test for significant changes to alpha diversity, and the Holm […]


Gymnosperms on the EDGE

Sci Rep
PMCID: 5902588
PMID: 29662101
DOI: 10.1038/s41598-018-24365-4
call_split See protocol

[…] EDGE values, and the resulting EDGE ranks.ED scores for all species of gymnosperms were obtained using the 100 ultrametric trees and were inferred using the function evol.distinct from the R package picante. The median value of all 100 resulting ED values for each species was compiled and used to produce the EDGE scores. Probability of extinction assessments were obtained from the IUCN Red List ( […]


Areas of high conservation value at risk by plant invaders in Georgia under climate change

Ecol Evol
PMCID: 5938453
PMID: 29760885
DOI: 10.1002/ece3.4005
call_split See protocol

[…] nd calculated the branch lengths for both trees with the program Phylocom Version 4.2 (Webb et al., ). We then calculated the mean pairwise distance (mpd) of the selected 114 endemic plants with the “picante” package (Blomberg, Garland & Ives, ; Kembel et al., ) in R (R Development Core Team, , Version 3.1.2) and compared it to a null distribution generated from 1,000 random sampling of 114 specie […]


Verrucomicrobia are prevalent in north temperate freshwater lakes and display class level preferences between lake habitats

PLoS One
PMCID: 5874073
PMID: 29590198
DOI: 10.1371/journal.pone.0195112
call_split See protocol

[…] tic relatedness of verrucomicrobial communities, standardized effect size mean pairwise distance (SES MPD; []) was calculated by comparing Faith’s index to a null model over 999 iterations. (ses.mpd, picante package []). While Faith’s index is positively correlated with richness, SES MPD is a measure of phylogenetic diversity that is unbiased by richness. Positive SES MPD values indicate more phyl […]


Competition matters: Determining the drivers of land snail community assembly among limestone karst areas in northern Vietnam

Ecol Evol
PMCID: 5916308
PMID: 29721286
DOI: 10.1002/ece3.3984

[…] morphological overdispersion and values smaller than zero indicated morphological clustering.The analyses of community structure were carried out using R version 3.4.0 (R Core Team ) with the package Picante 1.6‐2 (Kembel et al., ). […]

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Picante institution(s)
Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR, USA

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