Plant Comparative Genomics

Orthology Prediction and Phylogenetic Analysis Methods in Plants.- Species Tree Inference with SNP Data.- High-Throughput Evolutionary Comparative Analysis of Long Intergenic Non-Coding RNAs in Multiple Organisms.- NGS-Indel Coder v2.0: A Streamlined Pipeline to Code Indel Characters in Phylogenomic Data.- An SGSGeneloss-Based Method for Constructing a Gene Presence/Absence Table Using Mosdepth.- POInT: A Tool for Modeling Ancient Polyploidies Using Multiple Polyploid Genomes.- Searching for Homologous Genes Using Daisychain.- Detecting MicroRNAs in Plant Genomes with miRkwood.- Pangenome Analysis of Plant Transcripts and Coding Sequences.- Metagenomics Bioinformatic Pipeline.- Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach.- Applying Synteny Networks (SynNet) to Study Genomic Arrangements of Protein-Coding Genes in Plants.- Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis.- Isolation of Boechera stricta Developing Embryos for Hi-C.- Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens.- Use of Allele-Specific Amplification for Rapid Identification of Aromatic and Non-Aromatic Rice Germplasms.- Efficient Protein Extraction Protocols for NanoLC-MS/MS Proteomics Analysis of Plant Tissues with High Proteolytic Activity: A Case Study with Pineapple Pulp.