If you are using TrEase server for your publication, please cite:

Mishra, B., Ploch, S., Weiland, C. et al. The TrEase web service: inferring phylogenetic trees with ease. Mycol Progress 22, 84 (2023). https://doi.org/10.1007/s11557-023-01931-3

The softwares used in this server are as follows along with their citations. Please use the citations according to the pipeline you followed for your analyses.

For reference sequence search:
Blast X (Camacho et al. 2009).

For multiple sequence alignment:
mafft (Katoh et al. 2002) (Katoh and Standley 2013), Muscle (Edgar 2004), Prank (Loytynoja and Goldman 2005).

For alignment refinement:
Gblock (Castresana 2000).

For phylogenetic tree construction:
Raxml (Stamatakis 2014), FastTree (Price et al. 2010), MrBayes (Ronquist et al. 2012).

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC bioinformatics 10:421. doi:10.1186/1471-2105-10-421
Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular biology and evolution 17 (4):540-552
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research 32 (5):1792-1797. doi:10.1093/nar/gkh340
Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic acids research 30 (14):3059-3066
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution 30 (4):772-780. doi:10.1093/molbev/mst010
Loytynoja A, Goldman N (2005) An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences of the United States of America 102 (30):10557-10562. doi:10.1073/pnas.0409137102
Price MN, Dehal PS, Arkin AP (2010) FastTree 2--approximately maximum-likelihood trees for large alignments. PloS one 5 (3):e9490. doi:10.1371/journal.pone.0009490
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic biology 61 (3):539-542. doi:10.1093/sysbio/sys029
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30 (9):1312-1313. doi:10.1093/bioinformatics/btu033