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

Mishra B, Ploch S, Weiland C, Thines M (Unpublished manuscript) TrEase - a webserver to infer phylogenetic trees with ease. http://www.thines-lab.senckenberg.de/trease

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).
 
 
 
References:

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