update citations

Author: xonq

data/community/theiagen/rabies/all-clades/README.md

@@ -4,7 +4,7 @@ This is a minimal example dataset for *Lyssavirus rabies*.
 
 # Overview
 
-The phylogenetic tree was generated from all complete *Lyssavirus rabies* genomes obtained from [NCBI Nucleotide](https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNuclMetadata/) (accessed 2025/05/01) with > 95% unambiguous nucleotides and < 15,000 bp. Clade, subclade, and other associated metadata were acquired referencing the original rabies Nextstrain build and [RABV-GLUE's metadata](https://github.com/giffordlabcvr/RABV-GLUE/blob/master/tabular/reference-set-data.tsv). Clade- and subclade-specific mutations [were extracted for all monophyletic major and minor lineages](https://github.com/theiagen/utilities/pull/21), and disregarded for previously assigned clades that were not monophyletic in the phylogeny. Complete genome assemblies were aligned with `mafft v7.525` using default parameters and the phylogeny was reconstructed using `iqtree v2.4.0` with 1000 ultrafast bootstrap iterations and GTR+F+I+R7 selected as the evolutionary model by the *ModelFinder* module. A root node internal to the *L. rabies* phylogeny was selected by reconstructing an additional phylogeny using the same methodology with *L. australis* (NC_003243.1) and *L. gannoruwa* (KU244266.2) included as known outgroups ([Baynard & Fooks, 2021](https://www.sciencedirect.com/science/article/abs/pii/B9780128096338209369)).
+The phylogenetic tree was generated from all complete *Lyssavirus rabies* genomes obtained from [NCBI Nucleotide](https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNuclMetadata/) (accessed 2025/05/01) with > 95% unambiguous nucleotides and < 15,000 bp. Clade, subclade, and other associated metadata were acquired referencing the original rabies Nextstrain build and [RABV-GLUE's metadata](https://github.com/giffordlabcvr/RABV-GLUE/blob/master/tabular/reference-set-data.tsv). Clade- and subclade-specific mutations [were extracted for all monophyletic major and minor lineages](https://github.com/theiagen/utilities/pull/21), and disregarded for previously assigned clades that were not monophyletic in the phylogeny. Complete genome assemblies were aligned with `mafft v7.525` using default parameters and the phylogeny was reconstructed using `iqtree v2.4.0` with 1000 ultrafast bootstrap iterations and GTR+F+I+R7 selected as the evolutionary model by the *ModelFinder* module. A root node internal to the *L. rabies* phylogeny was selected by reconstructing an additional phylogeny using the same methodology with *L. australis* (NC_003243.1) and *L. gannoruwa* (KU244266.2) included as known outgroups ([Baynard & Fooks, 2021](doi.org/10.1016/B978-0-12-809633-8.20936-9)).
 
 # Metadata acquisition
 
@@ -113,4 +113,12 @@ t.set_outgroup(mrca)
 
 with open('rabv.rooted.newick', 'w') as out:
     out.write(t.write())
-```
+```
+
+# References
+
+- Troupin C, Dacheux L, Tanguy M, Sabeta C, Blanc H, Bouchier C, Vignuzzi M, Duchene S, Holmes E C, Bourhy H. Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts. PLoS Pathog 2016 Dec, 15;12(12):e1006041. doi:10.1371/journal.ppat.1006041.
+
+- Campbell F, Blank L, Cantrell A, Baxter S, Blackmore C, Dixon J, Goyder E. Factors that influence mental health of university and college students in the UK: a systematic review. BMC Public Health. 2022 Sep 20;22(1):1778. doi: 10.1186/s12889-022-13943-x.
+
+- Baynard A, Fooks A. Rabies and Other Lyssaviruses (Rhabdoviridae). Encyclopedia of Virology 2021 Mar, 1;4(1):738. doi:doi.org/10.1016/B978-0-12-809633-8.20936-9.