TY - JOUR AU - Edgar, R. C. AU - Batzoglou, S. PY - 2006 DA - 2006// TI - Multiple sequence alignment JO - Curr Opin Struct Biol VL - 16 UR - https://doi.org/10.1016/j.sbi.2006.04.004 DO - 10.1016/j.sbi.2006.04.004 ID - Edgar2006 ER - TY - JOUR AU - Thompson, J. D. AU - Plewniak, F. AU - Poch, O. PY - 1999 DA - 1999// TI - A comprehensive comparison of multiple sequence alignment programs JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.13.2682 DO - 10.1093/nar/27.13.2682 ID - Thompson1999 ER - TY - STD TI - BioEdit. [http://www.mbio.ncsu.edu/BioEdit/bioedit.html] UR - http://www.mbio.ncsu.edu/BioEdit/bioedit.html ID - ref3 ER - TY - STD TI - MPSA. [http://mpsa.ibcp.fr/] UR - http://mpsa.ibcp.fr/ ID - ref4 ER - TY - JOUR AU - Bentz, J. AU - Baucom, A. AU - Hansen, M. AU - Gregoret, L. PY - 1999 DA - 1999// TI - DINAMO: interactive protein alignment and model building JO - Bioinformatics VL - 15 UR - https://doi.org/10.1093/bioinformatics/15.4.309 DO - 10.1093/bioinformatics/15.4.309 ID - Bentz1999 ER - TY - JOUR AU - Clamp, M. AU - Cuff, J. AU - Searle, S. M. AU - Barton, G. J. PY - 2004 DA - 2004// TI - The Jalview Java alignment editor JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg430 DO - 10.1093/bioinformatics/btg430 ID - Clamp2004 ER - TY - JOUR AU - Deleage, G. AU - Combet, C. AU - Blanchet, C. AU - Geourjon, C. PY - 2001 DA - 2001// TI - ANTHEPROT: an integrated protein sequence analysis software with client/server capabilities JO - Comput Biol Med VL - 31 UR - https://doi.org/10.1016/S0010-4825(01)00008-7 DO - 10.1016/S0010-4825(01)00008-7 ID - Deleage2001 ER - TY - JOUR AU - Galtier, N. AU - Gouy, M. AU - Gautier, C. PY - 1996 DA - 1996// TI - SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny JO - Comput Appl Biosci VL - 12 ID - Galtier1996 ER - TY - JOUR AU - Nicholas, K. B. PY - 1997 DA - 1997// TI - GeneDoc: Analysis and Visualization of Genetic Variation JO - EMBNET NEWS VL - 4 ID - Nicholas1997 ER - TY - JOUR AU - Parry-Smith, D. J. AU - Payne, A. W. AU - Michie, A. D. AU - Attwood, T. K. PY - 1998 DA - 1998// TI - CINEMA–a novel colour INteractive editor for multiple alignments JO - Gene VL - 221 UR - https://doi.org/10.1016/S0378-1119(97)00650-1 DO - 10.1016/S0378-1119(97)00650-1 ID - Parry-Smith1998 ER - TY - STD TI - BELVU. [http://www.cgb.ki.se/cgb/groups/sonnhammer/Belvu.html] UR - http://www.cgb.ki.se/cgb/groups/sonnhammer/Belvu.html ID - ref11 ER - TY - JOUR AU - Barton, G. J. PY - 1993 DA - 1993// TI - ALSCRIPT: a tool to format multiple sequence alignments JO - Protein Eng VL - 6 UR - https://doi.org/10.1093/protein/6.1.37 DO - 10.1093/protein/6.1.37 ID - Barton1993 ER - TY - JOUR AU - Goodstadt, L. AU - Ponting, C. P. PY - 2001 DA - 2001// TI - CHROMA: consensus-based colouring of multiple alignments for publication JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.9.845 DO - 10.1093/bioinformatics/17.9.845 ID - Goodstadt2001 ER - TY - JOUR AU - Ilyin, V. A. AU - Pieper, U. AU - Stuart, A. C. AU - Marti-Renom, M. A. AU - McMahan, L. AU - Sali, A. PY - 2003 DA - 2003// TI - ModView, visualization of multiple protein sequences and structures JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/19.1.165 DO - 10.1093/bioinformatics/19.1.165 ID - Ilyin2003 ER - TY - JOUR AU - Li, W. AU - Godzik, A. PY - 2006 DA - 2006// TI - VISSA: a program to visualize structural features from structure sequence alignment JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl019 DO - 10.1093/bioinformatics/btl019 ID - Li2006 ER - TY - JOUR AU - Wang, Y. AU - Geer, L. Y. AU - Chappey, C. AU - Kans, J. A. AU - Bryant, S. H. PY - 2000 DA - 2000// TI - Cn3D: sequence and structure views for Entrez JO - Trends Biochem Sci VL - 25 UR - https://doi.org/10.1016/S0968-0004(00)01561-9 DO - 10.1016/S0968-0004(00)01561-9 ID - Wang2000 ER - TY - JOUR AU - Thompson, J. D. AU - Muller, A. AU - Waterhouse, A. AU - Procter, J. AU - Barton, G. J. AU - Plewniak, F. AU - Poch, O. PY - 2006 DA - 2006// TI - MACSIMS: multiple alignment of complete sequences information management system JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-318 DO - 10.1186/1471-2105-7-318 ID - Thompson2006 ER - TY - JOUR AU - Johnson, J. M. AU - Mason, K. AU - Moallemi, C. AU - Xi, H. AU - Somaroo, S. AU - Huang, E. S. PY - 2003 DA - 2003// TI - Protein family annotation in a multiple alignment viewer JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg021 DO - 10.1093/bioinformatics/btg021 ID - Johnson2003 ER - TY - STD TI - Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B: The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 2006, D187-191. 10.1093/nar/gkj161. 34 Database ID - ref19 ER - TY - JOUR AU - Berman, H. M. AU - Westbrook, J. AU - Feng, Z. AU - Gilliland, G. AU - Bhat, T. N. AU - Weissig, H. AU - Shindyalov, I. N. AU - Bourne, P. E. PY - 2000 DA - 2000// TI - The Protein Data Bank JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.235 DO - 10.1093/nar/28.1.235 ID - Berman2000 ER - TY - STD TI - Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T: Ensembl 2007. Nucleic Acids Res. 2007, D610-617. 10.1093/nar/gkl996. 35 Database ID - ref21 ER - TY - JOUR AU - Saitou, N. AU - Nei, M. PY - 1987 DA - 1987// TI - The neighbor-joining method: a new method for reconstructing phylogenetic trees JO - Mol Biol Evol VL - 4 ID - Saitou1987 ER - TY - JOUR AU - Zmasek, C. M. AU - Eddy, S. R. PY - 2001 DA - 2001// TI - ATV: display and manipulation of annotated phylogenetic trees JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.4.383 DO - 10.1093/bioinformatics/17.4.383 ID - Zmasek2001 ER - TY - STD TI - Jmol. [http://www.jmol.org/] UR - http://www.jmol.org/ ID - ref24 ER - TY - JOUR AU - Lee, B. AU - Richards, F. M. PY - 1971 DA - 1971// TI - The interpretation of protein structures: estimation of static accessibility JO - J Mol Biol VL - 55 UR - https://doi.org/10.1016/0022-2836(71)90324-X DO - 10.1016/0022-2836(71)90324-X ID - Lee1971 ER - TY - JOUR AU - Morgan, D. H. AU - Kristensen, D. M. AU - Mittelman, D. AU - Lichtarge, O. PY - 2006 DA - 2006// TI - an application for predicting and visualizing functional sites in protein structures JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl285 DO - 10.1093/bioinformatics/btl285 ID - Morgan2006 ER - TY - CHAP AU - Strang, G. PY - 1993 DA - 1993// TI - Orthogonality BT - Introduction to Linear Algebra PB - Wellesley-Cambridge Press CY - Wellesley, MA ID - Strang1993 ER -