[HTML][HTML] CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes

J Cheng, X Zeng, G Ren, Z Liu - BMC bioinformatics, 2013 - Springer
Background Chloroplast is an essential organelle in plants which contains independent
genome. Chloroplast genomes have been widely used for plant phylogenetic inference …

CPGView: A package for visualizing detailed chloroplast genome structures

S Liu, Y Ni, J Li, X Zhang, H Yang… - Molecular ecology …, 2023 - Wiley Online Library
Chloroplast genomes have been widely used in studying plant phylogeny and evolution.
Several chloroplast genome visualization tools have been developed to display the …

[HTML][HTML] A systematic comparison of chloroplast genome assembly tools

JA Freudenthal, S Pfaff, N Terhoeven, A Korte… - Genome Biology, 2020 - Springer
Background Chloroplasts are intracellular organelles that enable plants to conduct
photosynthesis. They arose through the symbiotic integration of a prokaryotic cell into an …

[HTML][HTML] CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome …

C Liu, L Shi, Y Zhu, H Chen, J Zhang, X Lin, X Guan - BMC genomics, 2012 - Springer
Background The complete sequences of chloroplast genomes provide wealthy information
regarding the evolutionary history of species. With the advance of next-generation …

Assembly, annotation and analysis of chloroplast genomes

X Zhong - 2020 - research-repository.uwa.edu.au
Chloroplast genome data is useful for phylogenetic analyses, for species identification and
for tracing evolutionary adaptations. Current sequencing technology enables us to obtain …

Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes

MR McKain, RH Hartsock, MM Wohl… - Bioinformatics, 2017 - academic.oup.com
Motivation Chloroplast genomes are now produced in the hundreds for angiosperm
phylogenetics projects, but current methods for annotation, alignment and tree estimation …

ChloroplastDB: the chloroplast genome database

L Cui, N Veeraraghavan, A Richter, K Wall… - Nucleic acids …, 2006 - academic.oup.com
Abstract The Chloroplast Genome Database (ChloroplastDB) is an interactive, web-based
database for fully sequenced plastid genomes, containing genomic, protein, DNA and RNA …

Reference-based assembly of chloroplast genome from leaf transcriptome data of Pterocarpus santalinus

S Senthilkumar, K Ulaganathan, M Ghosh Dasgupta - 3 Biotech, 2021 - Springer
Chloroplast genome sequencing is an essential tool to understand genome evolution and
phylogenetic relationship. The available methods for constructing chloroplast genome …

[PDF][PDF] The landscape of chloroplast genome assembly tools

JA Freudenthal, S Pfaff, N Terhoeven, A Korte… - bioRxiv, 2019 - researchgate.net
Chloroplasts are photosynthetic organelles in plant cells and contain their own genomic
information. That genome can be utilized in different scientific fields like phylogenetics or …

[HTML][HTML] Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species

C Guyeux, JC Charr, HTM Tran, A Furtado, RJ Henry… - PLoS …, 2019 - journals.plos.org
Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of
conservation in plants. Whole chloroplast genomes can now be readily obtained for plant …