Citing iTaxoTools
Main iTaxoTools citation:
Vences, M., Miralles, A., Brouillet, S., Ducasse, J., Fedosov, A., Kharchev, V., Kumari, S, Patmanidis, S., Puillandre, N., Scherz, M. D., Kostadinov, I., Renner, S. S. (2021). iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists. Megataxa 6: 77-92. https://www.mapress.com/mt/article/view/megataxa.6.2.1
Citation for "Concatenator":
Vences, M., S. Patmanidis, V. Kharchev & S.S. Renner (2022): Concatenator, a user-friendly program to concatenate DNA sequences, implementing graphical user interfaces for MAFFT and FastTree. Bioinformatics Advances 2: vbac050. https://doi.org/10.1093/bioadv/vbac050
.
The source code of all tools can be found on GitHub: https://github.com/iTaxoTools
Furthermore, when using one of the tools originating from other teams, please make sure to primarily cite the respective original papers. This refers to all tools for species delimitation and one tool for molecular diagnosis:
ASAP:
Puillandre, N., Brouillet, S. & Achaz, G. (2021) ASAP: assemble species by automatic partitioning.
Molecular Ecology Resources, 21: 609-620.
ABGD:
Puillandre, N., Lambert, A., Brouillet, S. & Achaz, G. (2012) ABGD, Automatic Barcode Gap Discovery
for primary species delimitation. Molecular Ecology, 21, 1864–1877.
DELINEATE:
Sukumaran, J., Holder, T.M. & Knowles, L.L. (2020) Incorporating the speciation process into species
delimitation. https://github.com/jeetsukumaran/delineate.
GMYC:
Pons, J., Barraclough, T.G., Gomez-Zurita, J., Cardoso, A., Duran, D.P., Hazell, S., Kamoun, S., Sumlin,
W.D. & Vogler, A.P. (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed
insects. Systematic Biology, 55, 595–609.
PTP:
Zhang J., Kapli P., Pavlidis P. & Stamatakis A. (2013) A general species delimitation method with
applications to phylogenetic placements. Bioinformatics, 29, 2869–2876.
TR2:\
Fujisawa, T., Aswad, A. & Barraclough, T.G. (2016) A rapid and scalable method for multilocus
species delimitation using Bayesian model comparison and rooted triplets. Systematic Biology, 65,
759–771
LIMES (calculation of indexes):
Ducasse, J., Ung, V., Lecointre, G. &
Miralles, A. (2020). LIMES: a tool for comparing species
partition. Bioinformatics, 36, 2282–2283.
LIMES (SPART
files handling):
Miralles, A., Ducasse, J., Brouillet, S., Flouri, T., Fujisawa, T., Kapli, P., Knowles, L.L., Kumari,
S., Stamatakis, A., Sukumaran, J., Lutteropp, S., Vences, M. & Puillandre, N. (2021). SPART, a
versatile and standardized data exchange format for species partition information. Molecular Ecology
Resources, https://doi.org/10.1111/1755-0998.13470
MolD:
Fedosov, A., Achaz, G. & Puillandre, N. (2019) Revisiting use of DNA characters in taxonomy with
MolD - a tree independent algorithm to retrieve diagnostic nucleotide characters from monolocus
datasets. bioRxiv, 838151; doi: https://doi.org/10.1101/838151
Furthermore, when using PYR8S, in many cases it will be appropriate to cite the original work by M.J. Sanderson on non-parametric rate smoothing and the r8s program:
Sanderson, M.J. (1997) A non-parametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution, 14, 1218–1231.
Sanderson, M.J. (2003) r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics, 19, 301–302.
And for the general concept of comparing sequences against a reference database using pairwise alignments in TaxI2, it might be appropriate to cite the paper introducing the original TaxI program:
TaxI / TaxI2 : Steinke, D., Salzburger, W., Vences, M. & Meyer, A. (2005) TaxI - A software tool for DNA barcoding using distance methods. – Philosophical Transactions of the Royal Society London, Ser. B, 360, 1975–1980.