GeSeq - Alternative Tools

Besides GeSeq several (more specialized) tools for (semi-)automatic annotation of organelle genomes are available. Please do not hesitate to contact us by email if you think your tool(s) should be listed here.

AGORA - organelle genome annotation

Jung J, Kim JI, Jeong Y-S and Yi G (2018) AGORA: organellar genome annotation from the amino acid and nucleotide references. Bioinformatics 34: 2661-2663


CGAP - chloroplast genome visualization, comparison and annotation

Cheng J, Zeng Xu, Ren G and Liu Z (2013) CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes. BMC Bioinformatics 14:95


Chloë - plant chloroplast genome annotation

Developed by the lab of Ian Small (PhD Thesis Xiao Zhong, 2020)


CPGAVAS and CPGAVAS2 - chloroplast genome annotation

Shi L, Chen H, Jiang M, Wang L, Wu X, Huang L and Liu C (2019) CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Research 47: W65-W73


Liu C, Shi L, Zhu Y, Chen H, Zhang J, Lin X and Guan X (2012) CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics 13: 715


DOGMA - plant chloroplast and animal mitochondrial genome annotation

Wyman SK, Jansen RK and Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255


MFannot - organelle genome annotation

Developed by the labs of B. Franz Lang and Gertraud Burger (unpublished)


MitoAnnotator​ - fish mitochondrial genome annotation

Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda, Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M and Nishida M (2013) MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Molecular Biology and Evolution 30: 2531-2540


MITOFY - plant mitochondrial genome annotation

Alverson AJ, Wei X, Rice DW, Stern DB, Barry K and Palmer JD (2010) Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Molecular Biology and Evolution 27: 1436-1448


MITOS - metazoan mitochondrial genome annotation

Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M and Stadler PF (2013) MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution 69: 313-319


MitoZ - animal mitochondrial genome assembly and annotation

Yang C, Meng G, Liu S and Li Y (2019). MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Research 47: e63


MOSAS - insect mitochondrial genome annotation

Sheffield NC, Hiatt KD, Valentine MC, Song H and Whiting MF (2010) Mitochondrial genomics in Orthoptera using MOSAS. Mitochondrial DNA 21: 87-104


ORG.Annotate - chloroplast genome annotation

Developed by Eric Coissac (unpublished)


PGA - chloroplast genome annotation

Qu X‑J, Moore MJ, Li D‑Z, Yi T‑S (2019) PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes. Plant Methods 15: 50


Plann - chloroplast genome annotation

Huang DI and Cronk QCB (2015) Plann: a command-line application for annotating plastome sequences. Applications in Plant Sciences 3: 1500026


Verdant - chloroplast genome annotation and phylogenetic analysis

McKain MR, Hartsock RH, Wohl MM and Kellogg EA (2017) Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes. Bioinformatics 33: 130-132