On Pattern-Cladistic Analyses Based on Complete Plastid Genome Sequences

Plastome Phylogenomics of Aucuba (Garryaceae)

(2022) Yuan Huang et al.   Frontiers in Genetics

Plastid Phylogenomic Analysis of Tordylieae Tribe (Apiaceae, Apioideae)

(2022) Tahir Samigullin et al.   Plants-Basel

Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae)

(2022) Ya-Ping Chen et al.   Frontiers in Plant Science

Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae)

(2021) Ju Namgung et al.   Scientific Reports

Highly Diverse Shrub Willows (Salix L.) Share Highly Similar Plastomes

(2021) Natascha D. Wagner et al.   Frontiers in Plant Science

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes

(2020) Xu Zhang et al.   BMC PLANT BIOLOGY

On the Typology of Relations

(2019) Evgeny V. Mavrodiev et al.   Evolutionary Biology

Background knowledge: the assumptions of pattern cladistics

(2019) Andrew V. Z. Brower   CLADISTICS

Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes

(2019) Deise J.P. Gonçalves et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts

(2019) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny of Diplazium (Athyriaceae) revisited: Resolving the backbone relationships based on plastid genomes and phylogenetic tree space analysis

(2019) Ran Wei et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

treespace : Statistical exploration of landscapes of phylogenetic trees

(2017) Thibaut Jombart et al.   Molecular Ecology Resources

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

A laid-back trip through the Hennigian Forests

(2017) Evgeny V. Mavrodiev et al.   PeerJ

Dealing with propositions, not with the characters: the ability of three-taxon statement analysis to recognise groups based solely on ‘reversals’, under the maximum-likelihood criteria

(2016) Evgeny V. Mavrodiev   AUSTRALIAN SYSTEMATIC BOTANY

Molecular homology and multiple-sequence alignment: an analysis of concepts and practice

(2015) David A. Morrison et al.   AUSTRALIAN SYSTEMATIC BOTANY

Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots

(2015) Craig F. Barrett et al.   NEW PHYTOLOGIST

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Homology assessment in parsimony and model-based analyses: two sides of the same coin

(2014) Leandro C. S. Assis   CLADISTICS

DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution

(2013) Xuhua Xia   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

TAXODIUM Version 1.0: A Simple Way to Generate Uniform and Fractionally Weighted Three-Item Matrices from Various Kinds of Biological Data

(2012) Evgeny V. Mavrodiev et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Quality measures for protein alignment benchmarks

(2010) Robert C. Edgar   NUCLEIC ACIDS RESEARCH

Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships

(2010) Jeffrey P. Townsend et al.   SYSTEMATIC BIOLOGY

Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci

(2009) E. Mossel et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Properties of Consensus Methods for Inferring Species Trees from Gene Trees

(2009) James H. Degnan et al.   SYSTEMATIC BIOLOGY

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS