Genome Assembly of the Polyclad Flatworm Prostheceraeus crozieri

Systematic errors in orthology inference and their effects on evolutionary analyses

(2021) Paschalis Natsidis et al.   iScience

Identifying and removing haplotypic duplication in primary genome assemblies

(2020) Dengfeng Guan et al.   BIOINFORMATICS

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

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Reinvestigating the early embryogenesis in the flatworm Maritigrella crozieri highlights the unique spiral cleavage program found in polyclad flatworms

(2019) Johannes Girstmair et al.   EvoDevo

NextPolish: a fast and efficient genome polishing tool for long-read assembly

(2019) Jiang Hu et al.   BIOINFORMATICS

Extraocular, rod-like photoreceptors in a flatworm express xenopsin photopigment

(2019) Kate A Rawlinson et al.   eLife

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms

(2018) Markus Alexander Grohme et al.   NATURE

Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians

(2018) Yang An et al.   Zoological Letters

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Efficient transgenesis and annotated genome sequence of the regenerative flatworm model Macrostomum lignano

(2017) Jakub Wudarski et al.   Nature Communications

New genes from old: asymmetric divergence of gene duplicates and the evolution of development

(2016) Peter W. H. Holland et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

HOX gene complement and expression in the planarian Schmidtea mediterranea

(2016) Ko W. Currie et al.   EvoDevo

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms

(2015) Bernhard Egger et al.   CURRENT BIOLOGY

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

Genome and transcriptome of the regeneration-competent flatworm,Macrostomum lignano

(2015) Kaja Wasik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

(2013) Gordon Gremme et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

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

Put a tiger in your tank: the polyclad flatworm Maritigrella crozieri as a proposed model for evo-devo

(2013) François Lapraz et al.   EvoDevo

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Planarian embryology in the era of comparative developmental biology

(2012) José M. Martín-Durán et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

(2011) Josep F Abril et al.   BMC GENOMICS

HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology

(2011) Ying-fu Zhong et al.   EVOLUTION & DEVELOPMENT

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Patterns of exon-intron architecture variation of genes in eukaryotic genomes

(2009) Liucun Zhu et al.   BMC GENOMICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

HomeoDB: a database of homeobox gene diversity

(2008) Ying-Fu Zhong et al.   EVOLUTION & DEVELOPMENT

Hox genes and the parasitic flatworms: New opportunities, challenges and lessons from the free-living

(2007) P.D. Olson   PARASITOLOGY INTERNATIONAL