rosids

rosids performs plastid genome–based phylogenomic analyses using publicly available plastome sequences and reproducible computational pipelines.

Key Features:

• Plastome Data Integration and Processing: Utilizes plastome sequences from 94 species available in GenBank and processes Illumina reads with bbtools for adaptor removal, phiX filtering, quality trimming, and contig assembly.
• Gene Alignment and Phylogenetic Inference: Aligns plastid genes using MAFFT and MACSE and performs phylogenetic reconstruction using Maximum Likelihood and Multispecies Coalescent methods with accuracy assessment.

Scientific Applications:

• Plastid Phylogenomics and Evolutionary Analysis: Supports evolutionary and systematics studies through robust inference of phylogenetic relationships from plastome data.

Methodology:

rosids implements a pipeline that processes Illumina sequencing reads with bbtools, assembles plastid contigs, aligns genes using MAFFT and MACSE, and infers phylogenies via Maximum Likelihood and Multispecies Coalescent frameworks with validation of inference accuracy.