Merge branch 'master' of https://github.com/VIB-PSB/ksrates

README.md

@@ -16,7 +16,7 @@ To position ancient WGD events with respect to speciation events in a phylogeny,
 
 *ksrates* is user-friendly command-line tool and [Nextflow](https://github.com/nextflow-io/nextflow) pipeline to compare paralog and ortholog *K*<sub>S</sub> distributions derived from genomic or transcriptomic sequences. *ksrates* estimates differences in synonymous substitution rates among the lineages involved and generates an adjusted mixed plot of paralog and ortholog *K*<sub>S</sub> distributions that allows to assess the relative phylogenetic positioning of presumed WGD and speciation events.
 
-For more details, see our [preprint](https://www.biorxiv.org/content/10.1101/2021.02.28.433234v1) and the documentation below.
+For more details, see the related [publication](https://doi.org/10.1093/bioinformatics/btab602) and the documentation below.
 
 ## Documentation
 
@@ -175,8 +175,7 @@ If you come across a bug or have any question or suggestion, please open an [iss
 
 If you publish results generated using *ksrates*, please cite:
 
-Sensalari, C., Maere, S., and Lohaus, R. (2021) *ksrates*: positioning whole-genome duplications relative to speciation events using rate-adjusted mixed paralog&ndash;ortholog *K*<sub>S</sub> distributions. *bioRxiv* 2021.02.28.433234 [doi: 10.1101/2021.02.28.433234](https://doi.org/10.1101/2021.02.28.433234)
->This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/content/what-unrefereed-preprint)].
+Sensalari C., Maere S. and Lohaus R. (2021) *ksrates*: positioning whole-genome duplications relative to speciation events in *K*<sub>S</sub> distributions. *Bioinformatics*, btab602, [doi: https://doi.org/10.1093/bioinformatics/btab602](https://doi.org/10.1093/bioinformatics/btab602)
 
 <!--
 ## Acknowledgements

doc/source/citation_acknowledgement.rst

@@ -4,4 +4,4 @@ How to cite us
 
 If you publish results generated using *ksrates*, please cite:
 
-Sensalari C., Maere S. and Lohaus R. (2021) *ksrates*: positioning whole-genome duplications relative to speciation events using rate-adjusted mixed paralog--ortholog  *K*:sub:`S` distributions. *bioRxiv* 2021.02.28.433234 `doi: https://doi.org/10.1101/2021.02.28.433234 <https://doi.org/10.1101/2021.02.28.433234>`__ 
+Sensalari C., Maere S. and Lohaus R. (2021) *ksrates*: positioning whole-genome duplications relative to speciation events in *K*:sub:`S` distributions. *Bioinformatics*, btab602, `doi: https://doi.org/10.1093/bioinformatics/btab602 <https://doi.org/10.1093/bioinformatics/btab602>`__

doc/source/concept.rst

@@ -9,7 +9,7 @@ However, when the lineages involved exhibit different substitution rates, the va
 
 *ksrates* is an open-source tool offering a rate-adjustment strategy that brings all the distributions to a common *K*:sub:`S` scale by compensating for the differences in synonymous substitution rates relative to the species of interest, the focal species. The final mixed plot produced by *ksrates* features rate-adjusted positions of the ortholog *K*:sub:`S` estimates of species divergence times that help to clarify the phylogenetic placement of WGDs inferred in the focal species.
 
-For more detail about the methodology, please see our `preprint <https://www.biorxiv.org/content/10.1101/2021.02.28.433234v1>`__.
+For more detail about the methodology, please see the related `publication <https://doi.org/10.1093/bioinformatics/btab602>`__.
 
 
 .. _`explained_example`: