plastome

Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

Plastid Genome Annotator

Organellar genome assembly

Bash scripts for analysis of Hyb-Seq data (from raw reads to species trees/networks)

The MitoGeneExtractor can be used to extract protein coding mitochondrial genes, such as COI and others from short and long read sequencing libraries.

Organelle Genome Assembler

Automated pipeline for assembly and annotation of plastid genomes

get chloroplast and mitochondrial genes from contigs of genome-skimming or transcriptome data

Chloroplast genome assembly, annotation and phylogenetic relationships of different populations of flowering plants

Population genomics, maternal plastid phylogeography, and cytonuclear discordance across global rice (Oryza sativa) germplasm.

Chloroplast genome (plastome) annotation from a FASTA: CDS, tRNA and rRNA, with GenBank/GFF3/FASTA output, per-feature provenance and a circular map.

R package for extracting chloroplast DNA barcode markers from GenBank plastomes, including rbcL, matK, and psbA-trnH.

Chloroplast genome structural region extractor (LSC/IRa/SSC/IRb) — published in PeerJ 2020