Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: TreeSim

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/TreeSim

Simulating Phylogenetic Trees
15 versions
Latest release: over 5 years ago
12 dependent packages
746 downloads last month

Papers Mentioning TreeSim 24

The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents
Cited by: 48
Author(s): Andrés Parada, Guillermo D’Elı́a, R. Eduardo Palma
Software Mentions: 9
Published: over 9 years ago

10.1371/journal.pone.0226949

A new, fast method to search for morphological convergence with shape data
Cited by: 32
Author(s): Silvia Castiglione, Carmela Serio, Davide Tamagnini, Marina Melchionna, Alessandro Mondanaro, Mirko Di Febbraro, Antonio Profico, Paolo Piras, Filippo Barattolo, Pasquale Raia
Software Mentions: 7
Published: almost 5 years ago

10.1111/2041-210X.12917

TreeSim <scp>GM</scp> : Simulating phylogenetic trees under general Bellman–Harris models with lineage‐specific shifts of speciation and extinction in R
Cited by: 17
Author(s): Oskar Hagen, Tanja Stadler
Software Mentions: 6
Published: about 7 years ago

10.3389/fgene.2014.00362

Patterns of diversification amongst tropical regions compared: a case study in Sapotaceae
Cited by: 31
Author(s): Kate Armstrong, Graham N. Stone, James A. Nicholls, Eugenio Valderrama, Arne A. Anderberg, Jenny E. E. Smedmark, Laurent Gautier, Yamama Naciri, Richard I. Milne, James E. Richardson
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pone.0088805

Molecular Phylogenetics and Temporal Diversification in the Genus Aeromonas Based on the Sequences of Five Housekeeping Genes
Cited by: 13
Author(s): J. Gaspar Lorén, Maribel Farfán, M. Carmen Fusté
Software Mentions: 5
Published: almost 11 years ago

10.1093/sysbio/syz080

The Implications of Lineage-Specific Rates for Divergence Time Estimation
Cited by: 15
Author(s): Tom Carruthers, Michael J. Sanderson, Robert W. Scotland
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0153570

If Dung Beetles (Scarabaeidae: Scarabaeinae) Arose in Association with Dinosaurs, Did They Also Suffer a Mass Co-Extinction at the K-Pg Boundary?
Cited by: 66
Author(s): Nicole L. Gunter, Tom A. Weir, Adam Slipinksi, Ladislav Bocäk, Stephen L. Cameron
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pcbi.1004409

Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation
Cited by: 116
Author(s): D. Ralph, F. A. Matsen
Software Mentions: 3
Published: almost 9 years ago

10.3389/fmicb.2017.00127

Evolutionary Roots and Diversification of the Genus Aeromonas
Cited by: 11
Author(s): Ariadna Sanglas, Vicenta Albarral, Maribel Farfán, J. Gaspar Lorén, M. Carmen Fusté
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pcbi.1005086

Likelihood-Based Inference of B Cell Clonal Families
Cited by: 86
Author(s): D. Ralph, F. A. Matsen
Software Mentions: 3
Published: about 8 years ago

10.3389/fgene.2020.00526

Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods
Cited by: 15
Author(s): Stéphane Guindon
Software Mentions: 3
Published: over 4 years ago

10.1093/sysbio/syv082

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees
Cited by: 116
Author(s): Diego Mallo, Leonardo de Oliveira Martins, David Posada
Software Mentions: 3
Published: about 9 years ago

10.1098/rsos.160681

Chemical antipredator defence is linked to higher extinction risk
Cited by: 2
Author(s): Kevin Arbuckle
Software Mentions: 3
Published: about 8 years ago

10.1111/jeb.12979

The impact of rate heterogeneity on inference of phylogenetic models of trait evolution
Cited by: 34
Author(s): Angela M. Chira, Gavin H. Thomas
Software Mentions: 3
Published: about 8 years ago

10.1093/sysbio/syx046

A Metric on Phylogenetic Tree Shapes
Cited by: 49
Author(s): Caroline Colijn, Giacomo Plazzotta
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.1003913

Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models
Cited by: 56
Author(s): Veronika Bošková, Sebastian Bonhoeffer, Tanja Stadler
Software Mentions: 2
Published: about 10 years ago

10.1371/currents.outbreaks.02bc6d927ecee7bbd33532ec8ba6a25f

Insights into the Early Epidemic Spread of Ebola in Sierra Leone Provided by Viral Sequence Data
Cited by: 68
Author(s): Tanja Stadler, Denise Kühnert, David A. Rasmussen, Louis du Plessis
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12862-015-0432-z

Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions
Cited by: 14
Author(s): Sacha Laurent, Marc Robinson‐Rechavi, Nicolas Salamin
Software Mentions: 2
Published: over 9 years ago

10.1098/rsfs.2019.0110

Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks
Cited by: 30
Author(s): Graham E. Budd, Richard P. Mann
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0076683

First Evidence for a Massive Extinction Event Affecting Bees Close to the K-T Boundary
Cited by: 24
Author(s): Sandra M. Rehan, Remko Leys, Michael P. Schwarz
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0025780

The Molecular Phylogenetic Signature of Clades in Decline
Cited by: 35
Author(s): Tiago B. Quental, Charles R. Marshall
Software Mentions: 1
Published: about 13 years ago

10.7717/peerj.4553

Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data
Cited by: 29
Author(s): Nicholas J. Matzke, Randall B. Irmis
Software Mentions: 1
Published: over 6 years ago

10.1093/bioinformatics/btab329

Improved inference of tandem domain duplications
Cited by: 0
Author(s): Chaitanya Aluru, Mona Singh
Software Mentions: 1
Published: over 3 years ago

10.1534/genetics.113.158808

Exact vs. Approximate Computation: Reconciling Different Estimates of Mycobacterium tuberculosis Epidemiological Parameters
Cited by: 17
Author(s): R. Zachariah Aandahl, Tanja Stadler, Scott A. Sisson, Mark M. Tanaka
Software Mentions: 1
Published: over 10 years ago