PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans

(2021) Eric D. Salomaki et al.   BMC BIOLOGY

Phylogenomic Insights into the Origin of Primary Plastids

(2021) Iker Irisarri et al.   SYSTEMATIC BIOLOGY

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

Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics.

(2019) Karen Siu-Ting et al.   MOLECULAR BIOLOGY AND EVOLUTION

New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

(2019) Jürgen F H Strassert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments

(2019) Raja Hashim Ali et al.   MOLECULAR BIOLOGY AND EVOLUTION

Non-photosynthetic predators are sister to red algae

(2019) Ryan M. R. Gawryluk et al.   NATURE

The New Tree of Eukaryotes

(2019) Fabien Burki et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group

(2018) Matthew W Brown et al.   Genome Biology and Evolution

Accelerated Estimation of Frequency Classes in Site-Heterogeneous Profile Mixture Models

(2018) Edward Susko et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria

(2018) Thomas Cavalier-Smith et al.   PROTOPLASMA

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

(2018) Xing-Xing Shen et al.   CELL

Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes

(2018) Gordon Lax et al.   NATURE

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

(2017) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group

(2016) Alexander K. Tice et al.   Biology Direct

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

BIR Pipeline for Preparation of Phylogenomic Data

(2015) Surendra Kumar et al.   Evolutionary Bioinformatics

Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

(2015) Li Song et al.   GigaScience

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

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

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Picomonas judraskeda Gen. Et Sp. Nov.: The First Identified Member of the Picozoa Phylum Nov., a Widespread Group of Picoeukaryotes, Formerly Known as ‘Picobiliphytes’

(2013) Ramkumar Seenivasan et al.   PLoS One

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS