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Guanliang MENG edited this page Dec 20, 2023 · 11 revisions

Citations

THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

WHEN YOU ADAPT (PART OF) THE SOFTWARE FOR YOUR USE CASES, THE AUTHOR AND THE SOFTWARE MUST BE EXPLICITLY CREDITED IN YOUR PUBLICATIONS AND SOFTWARE, AND YOU SHOULD ASK THE USERS OF YOUR SOFTWARE TO CITE THE SOFTWARE IN THEIR PUBLICATIONS. IN A WORD, 请讲武德.

COPYRIGHT 2019-2024 Guanliang Meng. ALL RIGHTS RESERVED.

When you use MitoZ, please cite:

  • Meng, G., Li, Y., Yang, C., & Liu, S. (2019). MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic acids research, 47(11), e63-e63. https://doi.org/10.1093/nar/gkz173

Additionally, you SHOULD also CITE related software invoked by MitoZ, without them, MitoZ will not make its way.

  • Fastp # for the all or filter subcommand (MitoZ version >= 3.0)

  • MitoAssemble (soapdenovo-trans) # for the all or assemble subcommand

    • Xie Y., Wu G., Tang J., Luo R., Patterson J., Liu S., Huang W., He G., Gu S., Li S. et al. . SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 2014; 30:1660–1666.

  • Megahit # for the all or assemble subcommand (MitoZ version >= 3.3)

    • Li, Dinghua, et al. "MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph." Bioinformatics 31.10 (2015): 1674-1676. https://doi.org/10.1093/bioinformatics/btv033

  • SPAdes # for the all or assemble or subcommand (MitoZ version >= 3.3)

  • tiara # for the all or assemble or findmitoscaf subcommand (MitoZ version >= 3.6)

    • Michał Karlicki, Stanisław Antonowicz, Anna Karnkowska, Tiara: deep learning-based classification system for eukaryotic sequences, Bioinformatics, Volume 38, Issue 2, January 2022, Pages 344–350, https://doi.org/10.1093/bioinformatics/btab672

  • HMMER # for the all or assemble or findmitoscaf subcommand

    • http://hmmer.org/
    • Wheeler T.J., Eddy S.R. nhmmer: DNA homology search with profile HMMs. Bioinformatics. 2013; 29:2487–2489.

  • Blast+ # for the all or assemble or findmitoscaf or annotate subcommand

    • Gertz E.M., Yu Y.K., Agarwala R., Schaffer A.A., Altschul S.F. Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol. 2006; 4:41.

  • Genewise # for the all or assemble or findmitoscaf or annotate subcommand

    • Birney E., Clamp M., Durbin R. GeneWise and Genomewise. Genome Res. 2004; 14:988–995.

  • Infernal # for the all or annotate subcommand

    • Nawrocki E.P., Eddy S.R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013; 29:2933–2935.

  • MiTFi # for the all or annotate subcommand

    • Juhling F., Putz J., Bernt M., Donath A., Middendorf M., Florentz C., Stadler P.F. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Res. 2012; 40:2833–2845.

  • Cricos # for the all or annotate or visualize subcommand

    • Krzywinski, Martin, et al. "Circos: an information aesthetic for comparative genomics." Genome research 19.9 (2009): 1639-1645.

  • BWA # for the all or annotate or visualize subcommand and you draw the sequencing coverage distribution track

    • Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25:1754–1760.

  • SAMtools # for the annotate or visualize subcommand and you draw the sequencing coverage distribution track

    • Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics. 2009; 25:2078–2079.

  • ete3 # for the all or assemble or findmitoscaf subcommand

    • ETE 3: Reconstruction, analysis and visualization of phylogenomic data. Jaime Huerta-Cepas, Francois Serra and Peer Bork. Mol Biol Evol 2016; doi: 10.1093/molbev/msw046

Please refer to the MitoZ paper and related publications for the reference details.

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