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Citations & References
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.. Note:: It is important that you cite T-Coffee when you use it. Citing us is (almost) like giving us money: it helps us convincing our institutions that what we do is useful and that they should keep paying our salaries and deliver donuts to our offices from time to time (Not that they ever did it, but it would be nice anyway). Cite the approriate web server if you use one, otherwise, cite the original paper from 2000 (By the way...NOOO, it was never named 'T-Coffee 2000').


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Comparative Genomics & Biology
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Erb, I., Notredame, C. **How should we measure proportionality on relative gene expression data?** Theory Biosci., 135(1-2):21-36 (2016), PMID26762323

Catuara-Solarz, S., Espinosa-Carrasco, J., Erb, I., Langohr, K., Gonzalez, J.R., Notredame, C., Dierssen, M. **Combined treatment with environmental enrichment and (-)-epigallocatchin-3-gallate ameliorates learning deficits and hippocampal alterations in a mouse model of Down syndrome**. eNeuro., 3(5)(2015) pii:ENEURO.0103, PMID:27844057

Di Tommaso, P., Palumbo, E., Chatzou, M., Prieto, P.,Heuer, M.L., Notredame, C. **The impact of Docker containers on ther performance of genomic pipelines**. PeerJ., 3:e1273 (2015), PMID:26421241

Catuara-Solarz, S., Espinosa-Carrasco, J., Erb, I., Langohr, K., Notredame, C., Gonzalez, J.R., Dierssen, M. **Principal component analysis of the effects of environmental enrichment and (-)-epigallocatchin-3-gallate on age-associated learning deficits in a mouse model of Down syndrome**. Front Behav. Neurosci., 9:330 (2015), PMID:26696850

Earl, D., Nguyen, N., Hickey, G., Harris, R.S., Fitzgerald, S., Beal, K. Seledtsov, I., Raney, B.J., Clawson, H., Kim, J., Kemena, C., Chang, J.-M., Erb, I., Poliakov, A., Hou, M., Herrero, J., Kent, W.J., Solovyev, V., Darling, A.E., Ma, J., Notredame, C., Brudno, M., Dubchak, I., Haussler, D., Paten, B. **Alignathon: a competitive assessment of whole-geome alignment methods**. Genome Res., 24(12):2077-2089 (2014), PMID:25273068

The mouse ENCODE Consortium. **A comparative encyclopedia of DNA elements in the mouse genome**.  Nature, 515(7527):355-364 (2014), PMID:25409824

Bussotti, G., Notredame, C., Enright, A.J. **Detecting and comparing non-coding RNAs in the high-throughput era**. Int. J. Mol. Sci., 14(8):15423-15458 (2013), PMID:23887659

Chang, J.-M., Taly, J.-F., Erb, I., Sung, T.Y., Hsu, W.L. Tang, C.Y., Notredame, C., Su, E.C. **Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations**. PLoS One, 8(10):e75542 (2013), PMID:24146760

Magis, C., van der Sloot, A.M., Serrano, L., Notredame, C. **An improved understanding of TNFL/TNFR interactions using structure-based classifications**. Trends Biochem. Sci., 37(9):353-363 (2012), PMID:22789664

Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D.G., Lagarde, J., Veeravalli, L., Ruan, X., Ruan, Y., Lassmann, T., Carninci, P., Brown, J.B., Lipovich, L., Gonzalez, J.M., Davis, C.A., Shiekhattar, R., Gingeras, T.R., Hubbard, T.J., Notredame, C., Harrow, J., Guigó, R. **The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution and expression**. Genome Res., 22(9):1775-1789 (2012), PMID:22955988

Breen, M.S., Kemena, C., Vlasov, P.K., Notredame, C., Kondrashov, F.A. **Epistasis as the primary factor in molecular evolution**. Nature, 490(7421), 535-538 (2012), PMID:23064225

Bussotti, G., Raineri, E., Erb, I., Zytnicki, M., Wilm, A., Beaudoing, E., Bucher, P., Notredame, C. **BlastR-fast and accurate database searches for non-coding RNAs**. Nucleic Acids Res., 39(16):6886-6895 (2011), PMID:21624887

Lin, H.N., Notredame, C., Chang, J.-M., Sung, T.Y., Hsu, W.L. **Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words**. PLoS One, 6(12):e27872, (2011), PMID:22163274

Ørom, U.A., Derrien, T., Beringer, M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Zytnicki, M., Notredame, C., Huang, Q., Guigo, R., Shiekhattar, R. **Long noncoding RNAs with enhancer-like function in human cells**. Cell, 143(1):46-58 (2010), PMID:20887892

Coll, O., Villalba, A., Bussotti, G., Notredame, C., Gebauer, F. **A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis**. Genes Dev., 24(2):129-134 (2010), PMID:20080951

Rausch, T., Emde, A.K., Weese, D., Döring, A., Notredame, C., Reinert, K. **Segment-based multiple sequence alignment**. Bioinformatics, 24(16):i187-i192 (2008), PMID:18689823

Dietmann, S:, Park, J., Notredame, C., Heger, A., Lappe, M., Holm, L. **A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3**. Nucleic Acids Res., 29(1):55-57 (2001), PMID:11125048


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T-Coffee Alignment Methods
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Kemena, C., Bussotti, G., Capriotti, E., Marti-Renom, M.A., Noredame, C. **Using tertiary structure for computation of highly accurate multiple RNA alignments with the SARA-Coffee package**. Bioinformatics, 29(9):1112-1119 (2013), PMID:234490094

Erb, I., González-Vallinas, J.R., Bussotti, G., Blanco, E., Eyras, E., Notredame, C. **Use of ChIP-Seq data for the design of a multiple promoter-alignment method**. Nucleic Acids Res., 40(7):e52 (2012), PMID:22230796

Chang, J.-M., Di Tommaso, P., Taly, J.-F., Notredame, C. **Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee**. BMC Bioinformatics, 13 Suppl 4:S1 (2012). PMID:22536955

Di Tommaso, P., Orobitg, M., Guirado, F., Cores, F., Espinosa, T., Notredame, C. **Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud**. Bioinformatics, 26(15):1903-1904 (2010). PMID:20605929

Wilm, A., Higgins, D.G., Notredame, C. **R-Coffee: a method for multiple alignment of non-coding RNA**. Nucleic Acids Res., 36(9):e52 (2008), PMID:18420654 

Armougom, F., Moretti, S., Poirot, O., Audic, S., Dumas, P., Schaeli, B., Keduas, V., Notredame. C. **Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee**. Nucleic Acids Res., 34:W604-W608 (2006), PMID:16845081

Wallace, I.M., O'Sullivan, O., Higgins, D.G., Notredame, C. **M-Coffee: combining multiple sequence alignment methods with T-Coffee**. Nucleic Acids Res., 34(6):1692-1699 (2006), PMID:16556910

O'Sullivan, O., Suhre, K., Abergel, C., Higgins, D.G., Notredame, C. **3DCoffee: combining protein sequences and structures within multiple sequence alignments**. J. Mol. Biol., 340(2):385-395 (2004). PMID: 15201059   

O'Sullivan, O., Zehnder, M., Higgins, D.G., Bucher, P., Grosdidier, A., Notredame, C. **APDB: a novel measure for benchmarking sequence alignment methods without reference alignments**. Bioinformatics, 19 Suppl 1:i215-i221 (2003). PMID:12855461

Notredame, C. **Mocca: semi-automatic method for domain hunting**. Bioinformatics, 17(4):373-374 (2001). PMID: 11301309

Notredame, C., Higgins, D.G., Heringa, J. **T-Coffee: A novel method for fast and accurate multiple sequence alignment**. J. Mol. Biol., 302(1):205-217 (2000). PMID: 10964570                                                                               

Notredame, C., Holm, L., Higgins, D.G. **COFFEE: an objective function for multiple sequence alignments**. Bioinformatics, 14(5):407-422 (1998). PMID: 968205


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T-Coffee Web Servers
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Floden, E.W., Tommaso, P.D., Chatzou, M., Magis, C., Notredame, C., Chang, J.-M. **PSI/TM-Coffee: a web server for fasta accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases**. Nucleic Acids Res., 44(W1):W339-W343 (2016). PMID:27106060

Chang, J.-M.\*, Tommaso P.\*, Lefort, V., Gascuel, O., Notredame, C. **TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction**. Nucleic Acids Research. 43(W1):W3-6 (2015). PMID: (*These two authors contribute equally)  

Di Tommaso, P., Bussotti, G., Kemena, C., Capriotti, E., Chatzou, M., Prieto, P., Notredame, C. **SARA-Coffee web server, a tool for computation of RNA sequence and structure multiple alignments**. Nucleic Acids Res., 42(Web Server issue):W356-W360 (2014). PMID:24972831 

Magis, C., Di Tommaso, P., Notredame, C. **T-RMSD: a web server for automated fine-grained protein structural classifcation**. Nucleic Acids Res., 41(Web Server issue):W358-W362 (2013). PMID:23716642

Rius, J., Cores, F., Solsona, F., van Hemert, J.I., Koetsier, J., Notredame, C. **A user-friendly web portal for T-Coffee on supercomputers**. BMC Bioinformatics, 12:150 (2011). PMID:21569428

Di Tommaso, P., Moretti, S., Xenarios, I., Orobitg, M., Montanyola, A., Chang, J.-M., Taly, J.-F., Notredame, C. **T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension**. Nucleic Acids Res., 39(Web Server issue):W13-W17 (2011). PMID:21558174

Moretti, S., Wilm, A., Higgins, D.G., Xenarios, I., Notredame, C. **R-Coffee: a web server for accurately aligning noncoding RNA sequences**., Nucleic Acids Res., 36(Web Server issue):W10-W13 (2008). PMID:18483080

Moretti, S., Armougom, F., Wallace, I.M., Higgins, D.G., Jongeneel, C.V., Notredame, C. **The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods**. Nucleic Acids Res., 35(Web Server issue):W645-W648 (2007). PMID:17526519

Moretti, S., Reinier, F., Poirot, O., Armougom, F., Audic, S., Keduas, V., Notredame, C. **PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments**. Nucleic Acids Res., 34(Web server issue):W600-W603 (2006), PMID:16845080

Armougom, F., Moretti, S., Keduas, V., Notredame, C. **The iRMSD: a local measure of sequence alignment accuracy using structural information**. Bioinformatics, 22(14):e35-e39 (2006). PMID:16873492

Armougom, F., Poirot, O., Moretti, S., Higgins, D.G., Bucher, P., Keduas, V., Notredame, C. **APDB: a web server to evaluate the accuracy of the sequence alignments using structural information**. Bioinformatics, 22(19):2439-2440 (2006). PMID:17032685

Claude, J.B., Suhre, K., Notredame, C., Claverie, J.M., Abergel C. **CaspR: a web server for automated molecular replacement using homology modelling**. Nucleic Acids Res., 32(Web Server issue):W606-9 (2004). PMID:15215460   
 
Poirot, O., Suhre, K., Abergel, C., O'Toole, E., Notredame, C. **3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment**. Nucleic Acids Res., 32(Web Server issue):W37-40 (2004). PMID: 15215345       

Poirot, O., O'Toole, E., Notredame, C. **Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments**. Nucleic Acids Res., Jul 1;31(13):3503-6 (2003). PMID: 12824354     
                                   

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T-Coffee Tools For MSA Evaluation
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Chang, J.-M., Tommaso, P., Notredame, C. **TCS: a new Multiple Sequence Alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction**. Molecular Biology and Evolution, 31(6):1625-37 (2014). PMID:24694831

Kemena, C., Taly, J.-F., Kleinjung, J., Notredame, C. **STRIKE: evaluation of protein MSAs using a single 3D structure**. Bioinformatics, 27(24):3385-3391 (2011). PMID:220339207

Magis, C., Stricher, F., van der Sloot, A.M., Serrano, L., Notredame, C. **T-RMSD: a fine-grained, structure based classification method and its application to the functional characterization of TNF receptors**. J. Mol. Biol., 400(3):605-617 (2010), PMID:20471393 

Armougom, F., Moretti, S., Keduas, V., Notredame, C. **The iRMSD: a local measure of sequence alignment accuracy using structural information**. Bioinformatics, 22(14):e35-e39 (2006), PMID:16873492


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Reviews, Briefings & Books
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Chatzou, M., Magis, C., Chang, J.-M., Kemena, C., Bussotti, G., Erb, I., Notredame, C. **Multiple sequence alignment modeling: methods and applications**. Brief Bioinform., pii: bbv099 (2015). PMID:26615024

Magis, C., Taly, J.-F., Bussotti, G., Chang, J.M., Di Tommaso, P., Erb, I., Espinosa-Carrasco, J., Notredame, C. **T-Coffee: tree-based consistency objective function for alignment evaluation**. Methods Mol. Biol., 1079:117-129 (2014). PMID:24170398

Taly, J.-F.\*, Magis, C.\*, Bussotti, G., Chang, J.-M., Di Tommaso, P., Erb, I., Espinosa-Carrasco, J., Kemena, C., Notredame, C. **Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures**. Nature Protocols, 1669-1682 (2011), PMID:21979275 (*These two authors contribute equally) 

Notredame, C. **Computing multiple sequence/structure alignments with the T-Coffee package**. Curr. Protoc. Bioinformatics, Chapter 3, Unit 3.8.1-25 (2010). PMID:20205190

Kemena, C., Notredame, C. **Upcoming challenges for multiple sequence alignment methods in the high-throughput era**. Bioinformatics, 25(19):2455-2465 (2009). PMID:19648142

Notredame, C. **Recent evolutions of multiple sequence alignment algorithms**. PLoS Comput. Biol., 3(8):e123 (2007). PMID:17784778

Notredame, C., Suhre, K. **Computing multiple sequence/structure alignments with the T-Coffee package**. Curr. Protoc. Bioinformatics, Chapter 3:Unit 3.8 (2004), PMID:18428722

Notredame, C., Abergel, C. **Using multiple alignment methods to assess the quality of genomic data analysis**. In: Andrade MA, editor. Bioinformatics and genomes: current perspectives. Wymondham (UK): Horizon Scientific Press,30–50 (2003).   

Notredame, C. **Recent progress in multiple sequence alignment: a survey**. Pharmacogenomics, 3(1):131-144 (2002). PMID:11966409