[DOC] Replaced preprint with journal version

Author: cpockrandt

README.rst

@@ -28,15 +28,15 @@ annotate GFF/GTF files with PhyloCSF and its confidence scores.
 
 If you find our implementation useful and use it in your work, please consider citing it:
 
-    Christopher Pockrandt, Martin Steinegger, Steven Salzberg. **PhyloCSF++: A fast and user-friendly implementation of PhyloCSF with annotation tools**. `bioRxiv`_, 2021.
+    Christopher Pockrandt, Martin Steinegger, Steven Salzberg. **PhyloCSF++: A fast and user-friendly implementation of PhyloCSF with annotation tools**. `Bioinformatics`_, 2021.
 
 Please also consider citing the original method papers:
 
     Lin MF et al. PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions. Bioinformatics, 2011.
 
     Mudge JM et al. Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. Genome Research, 2019.
 
-.. _bioRxiv: https://doi.org/10.1101/2021.03.10.434297
+.. _Bioinformatics: https://doi.org/10.1093/bioinformatics/btab756
 
 Installation
 ^^^^^^^^^^^^

src/phylocsf++.cpp

@@ -23,7 +23,7 @@ int main(int argc, char **argv)
                   "For documentation and help, check out https://github.com/cpockrandt/PhyloCSFpp\n\n"
                   "Please consider citing:\n"
                   "  Pockrandt et al., PhyloCSF++: A fast and user-friendly implementation of PhyloCSF\n"
-                  "  with annotation tools, https://doi.org/10.1101/2021.03.10.434297, bioRxiv 2021");
+                  "  with annotation tools, https://doi.org/10.1093/bioinformatics/btab756, Bioinformatics 2021");
 
     args.add_subprogram("build-tracks", "Computes PhyloCSF and Power tracks for each codon and all 6 frames from alignments from MAF files. Outputs them in wig files.");
     args.add_subprogram("score-msa", "Computes PhyloCSF scores, ancestral sequence composition sores and branch length scores for entire alignments from MAF files. Outputs them in a BED-like format.");