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phyloGenerator specifications

Information


Unique identifier OMICS_08680
Name phyloGenerator
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License Apache License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline William D. Pearse

Publication for phyloGenerator

phyloGenerator citations

 (6)
library_books

Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field

2017
Front Microbiol
PMCID: 5732146
PMID: 29321763
DOI: 10.3389/fmicb.2017.02414

[…] de Database. Amaranthus powellii was not represented and sequences from congeneric A. viridis were used instead. Sequences were aligned and checked in Unipro UGENE () and a tree was constructed using phyloGenerator with Ginkgo biloba used as an outgroup (). A distance matrix was derived using the cophenetic.phylo function in the R package “ape” (). We expected little intraspecific variation in chl […]

call_split

Phylogenetic conservatism and trait correlates of spring phenological responses to climate change in northeast China

2017
Ecol Evol
PMCID: 5587463
PMID: 28904756
DOI: 10.1002/ece3.3207
call_split See protocol

[…] We built a phylogenetic tree based on DNA sequence data, which were collected from GenBank for 47 species (90% and 94% species for flowering and leafing phenology, respectively). We used the program phyloGenerator2 (Pearse & Purvis, ) to download, align, and concatenate sequence data from GenBank for the following markers: atp1, atpB, matR, rbcL, matK, psbA, ITS, ndhF, trnL‐trnF. There were a tot […]

call_split

Plant performance was greater in the soils of more distantly related plants for an herbaceous understory species

2017
PMCID: 5499765
PMID: 28702162
DOI: 10.1093/aobpla/plx005
call_split See protocol

[…] arch in Garli (; version 0.951) and branch lengths are in substitutions per site (). The result is a phylogram with fine-scale variation in phylogenetic distances among species pairs. Second, we used phyloGenerator’s () congeneric.merge function, which matches species in our sampled species list to genera on the global angiosperm phylogeny of . Because the genus Anemonella was not present in this […]

library_books

Beyond the EDGE with EDAM: Prioritising British Plant Species According to Evolutionary Distinctiveness, and Accuracy and Magnitude of Decline

2015
PLoS One
PMCID: 4446313
PMID: 26018568
DOI: 10.1371/journal.pone.0126524

[…] s above have been released onto GenBank [] (see for accession numbers), but only 364 of them were used for this project. An additional 312 different rbcL sequences were downloaded from GenBank using phyloGenerator [], meaning the alignment altogether represents 91% of native genera in Britain (according to PLANTATT; []). We constructed a family-level constraint tree based on the APG III classific […]

call_split

Predicting climate change effects on wetland ecosystem services using species distribution modeling and plant functional traits

2015
PMCID: 4288999
PMID: 25576286
DOI: 10.1007/s13280-014-0593-9
call_split See protocol

[…] h the majority from the LEDA traitbase (Kleyer et al. ; Electronic Supplementary Material, Table S3). Gaps in trait data were filled with estimates based on phylogenetic relationships (generated with phyloGenerator) using PhyloPars (Bruggeman et al. ). This approach resulted in complete datasets for the continuous traits: specific leaf area (SLA), canopy height (CH), and root depth (RD) (Table ). […]

library_books

Colony size is linked to paternity frequency and paternity skew in yellowjacket wasps and hornets

2014
BMC Evol Biol
PMCID: 4298054
PMID: 25547876
DOI: 10.1186/s12862-014-0277-x

[…] We generated a phylogenetic hypothesis for our dataset using phyloGenerator [] based largely on molecular data reported in two recent studies of vespine phylogeny [,] (Genbank accession numbers available in Additional file : Table S5). Sequences were aligned wi […]

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phyloGenerator institution(s)
Department of Life Sciences, Imperial College London, Ascot, UK

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