Phyldog statistics

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Phyldog specifications

Information


Unique identifier OMICS_06052
Name Phyldog
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
Parallelization MPI
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Phyldog

Phyldog in publications

 (12)
PMCID: 5123345
PMID: 28185583
DOI: 10.1186/s12859-016-1268-2

[…] reconstruction [, ]. species-tree aware methods are sensitive to errors in reconstructed species trees; however, resources such as timetree [] and recent species tree reconstruction methods, such as phyldog and mixtreem [, ], appears to be sufficiently reliable., for future work, extending the model to incorporate even more biological knowledge is of interest. in particular, being able […]

PMCID: 4971187
PMID: 27481787
DOI: 10.1098/rstb.2015.0335

[…] of gene trees and species trees, but also of other important parameters such as population sizes under complex population dynamics [,] and divergence times using relaxed-clock models [,]., phyldog [] relies on a birth–death probabilistic approach to jointly reconstruct species and gene trees from multiple gene family alignments., most species tree reconstruction methods rely either […]

PMCID: 4915358
PMID: 27016024
DOI: 10.1093/molbev/msw057

[…] the brassica rapa genome () was used in place of the phytozome version as there were restrictions on the use of the later. orthologous gene groups (orthogroups) were inferred using orthofinder (). phyldog () was used to simultaneously infer the gene trees for each orthogroup and reconcile them with the species phylogeny (supplementary fig. s1a, supplementary material online). the topology […]

PMCID: 4603753
PMID: 26450506
DOI: 10.1186/1471-2164-16-S10-S1

[…] hgt+ils. there are also methods designed to infer species trees in the presence of gene tree discordance resulting from duplication and loss, and it is possible that some of these methods (e.g., phyldog [] and mixtreem []) might have good accuracy under the msc. future work should also explore ca-ml using different ml heuristics (e.g., phyml [], nhphyml [], iqtree []) and under more complex […]

PMCID: 4603630
PMID: 26452018
DOI: 10.1186/1471-2105-16-S14-S5

[…] conditional probabilities mixing two models., • integrate the model into an integrative probabilistic model of genome evolution, handling both sequence evolution and gene content evolution, like phyldog []., • with this integration the model can be used to infer species phylogenies, or at least in the current state of computational complexity, to test among a small number of species […]


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Phyldog institution(s)
Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France

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