From e4e5f039e0ffbbc2e9d4cc0768779e513b67f559 Mon Sep 17 00:00:00 2001 From: Christopher Pockrandt Date: Tue, 4 Jan 2022 16:38:18 +0100 Subject: [PATCH] [DOC] Replaced preprint with journal version --- README.rst | 4 ++-- src/phylocsf++.cpp | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index 04f75d8..8508924 100644 --- a/README.rst +++ b/README.rst @@ -28,7 +28,7 @@ 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: @@ -36,7 +36,7 @@ Please also consider citing the original method papers: 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 ^^^^^^^^^^^^ diff --git a/src/phylocsf++.cpp b/src/phylocsf++.cpp index 6455bd8..670c278 100644 --- a/src/phylocsf++.cpp +++ b/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.");