4.7 Article

Comparative analyses and phylogenetic relationships of thirteen Pholidota species (Orchidaceae) inferred from complete chloroplast genomes

Related references

Note: Only part of the references are listed.
Article Genetics & Heredity

Comparative Chloroplast Genomics and Phylogenetic Analysis of Thuniopsis and Closely Related Genera within Coelogyninae (Orchidaceae)

Lin Li et al.

Summary: This study sequenced and analyzed the complete chloroplast genomes of Thuniopsis cleistogama and Thunia alba. The results revealed the role of natural selection in their evolution and identified the main reason for chloroplast genome size variation. Additionally, this research provides valuable insights into the classification and evolution of orchids.

FRONTIERS IN GENETICS (2022)

Article Biochemistry & Molecular Biology

ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

Diego Darriba et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biotechnology & Applied Microbiology

Selection constraints determine preference for A/U-ending codons in Taxus contorta

Aasim Majeed et al.

GENOME (2020)

Article Biochemistry & Molecular Biology

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

Chengjie Chen et al.

MOLECULAR PLANT (2020)

Article Biochemistry & Molecular Biology

OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes

Stephan Greiner et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemical Research Methods

IRscope: an online program to visualize the junction sites of chloroplast genomes

Ali Amiryousefi et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution

Wan-Lin Dong et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2018)

Article Biochemistry & Molecular Biology

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

Julio Rozas et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemical Research Methods

ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

GeSeq - versatile and accurate annotation of organelle genomes

Michael Tillich et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Plant Sciences

The chloroplast genome sequence from Eugenia uniflora, a Myrtaceae from Neotropics

Maria Eguiluz et al.

PLANT SYSTEMATICS AND EVOLUTION (2017)

Article Biochemical Research Methods

MISA-web: a web server for microsatellite prediction

Sebastian Beier et al.

BIOINFORMATICS (2017)

Review Biotechnology & Applied Microbiology

Chloroplast genomes: diversity, evolution, and applications in genetic engineering

Henry Daniell et al.

GENOME BIOLOGY (2016)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Multidisciplinary Sciences

Ecological and evolutionary significance of genomic GC content diversity in monocots

Petr Smarda et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Genetics & Heredity

Repetitive Sequences in Plant Nuclear DNA: Types, Distribution, Evolution and Function

Shweta Mehrotra et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

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

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Multidisciplinary Sciences

Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L

Dong-Keun Yi et al.

PLOS ONE (2012)

Article Evolutionary Biology

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

Fredrik Ronquist et al.

SYSTEMATIC BIOLOGY (2012)

Review Ecology

Phylogenetic evidence for pollinator-driven diversification of angiosperms

Timotheues van der Niet et al.

TRENDS IN ECOLOGY & EVOLUTION (2012)

Article Biotechnology & Applied Microbiology

Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles

Maya Botzman et al.

GENOME BIOLOGY (2011)

Article Biochemical Research Methods

Interactive microbial genome visualization with GView

Aaron Petkau et al.

BIOINFORMATICS (2010)

Review Plant Sciences

An update on chloroplast genomes

V. Ravi et al.

PLANT SYSTEMATICS AND EVOLUTION (2008)

Article Plant Sciences

9,10-dihydrophenanthrene derivatives from Pholidota yunnanensis and scavenging activity on DPPH free radical

X.-Y. Guo et al.

JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH (2007)

Article Chemistry, Medicinal

Stilbene derivatives from Pholidota chinensis and their anti-inflammatory activity

Jue Wang et al.

CHEMICAL & PHARMACEUTICAL BULLETIN (2006)

Article Biochemistry & Molecular Biology

VISTA: computational tools for comparative genomics

KA Frazer et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemical Research Methods

Automatic annotation of organellar genomes with DOGMA

SK Wyman et al.

BIOINFORMATICS (2004)

Review Genetics & Heredity

Microsatellites: Simple sequences with complex evolution

H Ellegren

NATURE REVIEWS GENETICS (2004)

Article Biochemistry & Molecular Biology

The role of context-dependent mutations in generating compositional and codon usage bias in grass chloroplast DNA

BR Morton

JOURNAL OF MOLECULAR EVOLUTION (2003)

Article Biochemistry & Molecular Biology

LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA

M Brudno et al.

GENOME RESEARCH (2003)

Article Biochemistry & Molecular Biology

REPuter: the manifold applications of repeat analysis on a genomic scale

S Kurtz et al.

NUCLEIC ACIDS RESEARCH (2001)