# nf-core/proteinfamilies: Citations

## [nf-core/proteinfamilies](https://www.biorxiv.org/content/10.1101/2025.08.12.670010/)

> Karatzas E, Beracochea M, Baltoumas FA, Aplakidou E, Richardson L, Fellows Yates JA, Lundin D, nf-core community, Buluc A, Kyrpides N, Georgakopoulos-Soares I. nf-core/proteinfamilies: A scalable pipeline for the generation of protein families. bioRxiv. 2025:2025-08. doi: 10.1101/2025.08.12.670010.

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [SeqFu](https://pubmed.ncbi.nlm.nih.gov/34066939/)

> Telatin A, Fariselli P, Birolo G. SeqFu: a suite of utilities for the robust and reproducible manipulation of sequence files. Bioengineering. 2021 May 7;8(5):59. doi: 10.3390/bioengineering8050059. PubMed PMID: 34066939; PubMed Central PMCID: PMC8148589.

- [SeqKit](https://pubmed.ncbi.nlm.nih.gov/38898985/)

> Shen W, Sipos B, Zhao L. SeqKit2: A Swiss army knife for sequence and alignment processing. iMeta. 2024 Apr 5:e191. doi: 10.1002/imt2.191. PubMed PMID: 38898985; PubMed Central PMCID: PMC11183193.

- [MMseqs2](https://pubmed.ncbi.nlm.nih.gov/33734313/)

> Mirdita M, Steinegger M, Breitwieser F, Söding J, Levy Karin E. Fast and sensitive taxonomic assignment to metagenomic contigs. Bioinformatics. 2021 Sep 15;37(18):3029-31. doi: 10.1093/bioinformatics/btab184. PubMed PMID: 33734313; PubMed Central PMCID: PMC8479651.

- [FAMSA](https://pubmed.ncbi.nlm.nih.gov/27670777/)

> Deorowicz S, Debudaj-Grabysz A, Gudyś A. FAMSA: Fast and accurate multiple sequence alignment of huge protein families. Scientific reports. 2016 Sep 27;6(1):33964. doi: 10.1038/srep33964. PubMed PMID: 27670777; PubMed Central PMCID: PMC5037421.

- [mafft](https://pubmed.ncbi.nlm.nih.gov/23329690/)

> Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution. 2013 Jan 16;30(4):772-80. doi: 10.1093/molbev/mst010. PubMed PMID: 23329690; PubMed Central PMCID: PMC3603318.

- [ClipKIT](https://pubmed.ncbi.nlm.nih.gov/33264284/)

> Steenwyk JL, Buida III TJ, Li Y, Shen XX, Rokas A. ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. PLoS biology. 2020 Dec 2;18(12):e3001007. doi: 10.1371/journal.pbio.3001007. PubMed PMID: 33264284; PubMed Central PMCID: PMC7735675.

- [hmmer](https://pubmed.ncbi.nlm.nih.gov/29905871/)

> Eddy SR. Accelerated profile HMM searches. PLoS computational biology. 2011 Oct 20;7(10):e1002195. doi: 10.1371/journal.pcbi.1002195. PubMed PMID: 22039361; PubMed Central PMCID: PMC3197634.

- [HH-suite3](https://pubmed.ncbi.nlm.nih.gov/31521110/)

> Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger SJ, Söding J. HH-suite3 for fast remote homology detection and deep protein annotation. BMC bioinformatics. 2019 Dec;20:1-5. doi: 110.1186/s12859-019-3019-7. PubMed PMID: 31521110; PubMed Central PMCID: PMC6744700.

- [Biopython](https://pubmed.ncbi.nlm.nih.gov/19304878/)

> Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, De Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009 Jun 6;25(11):1422. doi: 10.1093/bioinformatics/btp163. PubMed PMID: 19304878; PubMed Central PMCID: PMC2682512.

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
