Picante protocols

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Picante specifications

Information


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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Publication for Picante

Picante in pipelines

 (7)
2018
PMCID: 5821391
PMID: 29420542
DOI: 10.1371/journal.pntd.0006248

[…] down without further links of the parasites to the remaining hosts. we built and obtained indexes of the network structure on the r programming environment [] using the igraph [], bipartite [], and picante [] packages. the resilience of the networks of each genus and stage of ticks after recursive removal of host nodes was evaluated with the package netswan for r []. visualization […]

2018
PMCID: 5843337
PMID: 29518170
DOI: 10.1371/journal.pone.0194131

[…] performed in a pair-wise fashion between samples using bonferroni correction on p-values., data analysis was performed using r statistical software [] with the packages vegan [], phyloseq [] and picante []. furthermore, deseq2 [] was used to highlight otus differentially present among different instars of c. capitata, and when collected from different host fruits., clustering produced 3,169 […]

2017
PMCID: 5240445
PMID: 28095877
DOI: 10.1186/s40168-016-0220-z

[…] data. all p values were adjusted for multiple comparisons with the false discovery rate (fdr) correction using the benjamini-hochberg method []. we made use of the r packages vegan v2.3-5 [], picante v1.6-2 [], and the bioconductor package phyloseq v1.14 []., detailed information regarding isolation, sequencing, and taxonomic assignment of bacteria isolates is available in additional file […]

2016
PMCID: 4841225
PMID: 27114865
DOI: 10.7717/peerj.1882

[…] of phylogenetic signal. k values closer to zero correspond to a random or convergent pattern of evolution, while k values greater than 1 indicate strong phylogenetic signal. we used the r package ‘picante’ () to compute k and the significance test. to test the possible decrease of power or the randomization test due to the low number of species in bilimneus (15, vs. 50 in limnebius s.str.) […]

2016
PMCID: 4936053
PMID: 27388460
DOI: 10.1186/s40168-016-0181-2

[…] acids with default settings. bootstrap support was derived from 100 replicates, also implemented within mingle. phylogenetic diversity scores for susc and susd gene trees were calculated using the picante r package []. all trees were visually inspected using arb v6.0.2 []., genomes were annotated using prokka v1.11 []. all subsequent gene-based analysis was performed using the output […]


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Picante in publications

 (281)
PMCID: 5934361
PMID: 29725049
DOI: 10.1038/s41467-018-04218-4

[…] 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 […]

PMCID: 5919903
PMID: 29700420
DOI: 10.1038/s41598-018-24931-w

[…] 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, […]

PMCID: 5902588
PMID: 29662101
DOI: 10.1038/s41598-018-24365-4

[…] 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 […]

PMCID: 5938453
PMID: 29760885
DOI: 10.1002/ece3.4005

[…] 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 […]

PMCID: 5874073
PMID: 29590198
DOI: 10.1371/journal.pone.0195112

[…] 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 […]


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

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