TY - JOUR AU - Anisimova, M. AU - Cannarozzi, G. AU - Liberles, D. A. PY - 2010 DA - 2010// TI - Finding the balance between the mathematical and biological optima in multiple sequence alignment JO - Trends in Evolutionary Biol VL - 2 UR - https://doi.org/10.4081/eb.2010.e7 DO - 10.4081/eb.2010.e7 ID - Anisimova2010 ER - TY - JOUR AU - Lee, C. AU - Grasso, C. AU - Sharlow, M. F. PY - 2002 DA - 2002// TI - Multiple sequence alignment using partial order graphs JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.3.452 DO - 10.1093/bioinformatics/18.3.452 ID - Lee2002 ER - TY - JOUR AU - Löytynoja, A. AU - Goldman, N. PY - 2005 DA - 2005// TI - An algorithm for progressive multiple alignment of sequences with insertions JO - Proc National Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0409137102 DO - 10.1073/pnas.0409137102 ID - Löytynoja2005 ER - TY - CHAP AU - Löytynoja, A. AU - Vilella, A. J. AU - Goldman, N. PY - 2012 DA - 2012// TI - Accurate Extension of Multiple Sequence Alignments Using a Phylogeny-Aware Graph Algorithm BT - Bioinformatics ID - Löytynoja2012 ER - TY - JOUR AU - Gascuel, O. PY - 1997 DA - 1997// TI - BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data JO - Mol Biol Evol VL - 14 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025808 DO - 10.1093/oxfordjournals.molbev.a025808 ID - Gascuel1997 ER - TY - JOUR AU - Stuart, G. W. AU - Moffett, K. AU - Baker, S. PY - 2002 DA - 2002// TI - Integrated gene and species phylogenies from unaligned whole genome protein sequences JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.1.100 DO - 10.1093/bioinformatics/18.1.100 ID - Stuart2002 ER - TY - JOUR AU - Thorne, J. L. AU - Goldman, N. AU - Jones, D. T. PY - 1996 DA - 1996// TI - Combining protein evolution and secondary structure JO - Mol Biol Evol VL - 13 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025627 DO - 10.1093/oxfordjournals.molbev.a025627 ID - Thorne1996 ER - TY - JOUR AU - Szalkowski, A. M. AU - Anisimova, M. PY - 2011 DA - 2011// TI - Markov Models of Amino Acid Substitution to Study Proteins with Intrinsically Disordered Regions JO - PLoS ONE VL - 6 UR - https://doi.org/10.1371/journal.pone.0020488 DO - 10.1371/journal.pone.0020488 ID - Szalkowski2011 ER - TY - JOUR AU - Biegert, A. AU - Söding, J. PY - 2009 DA - 2009// TI - Sequence context-specific profiles for homology searching JO - Proc National Acad Sci VL - 106 UR - https://doi.org/10.1073/pnas.0810767106 DO - 10.1073/pnas.0810767106 ID - Biegert2009 ER - TY - JOUR AU - Needleman, S. B. AU - Wunsch, C. D. PY - 1970 DA - 1970// TI - A general method applicable to the search for similarities in the amino acid sequence of two proteins JO - J Mol Biol VL - 48 UR - https://doi.org/10.1016/0022-2836(70)90057-4 DO - 10.1016/0022-2836(70)90057-4 ID - Needleman1970 ER - TY - JOUR AU - Gotoh, O. PY - 1982 DA - 1982// TI - An improved algorithm for matching biological sequences JO - J Mol Biol VL - 162 UR - https://doi.org/10.1016/0022-2836(82)90398-9 DO - 10.1016/0022-2836(82)90398-9 ID - Gotoh1982 ER - TY - JOUR AU - Viterbi, A. PY - 1967 DA - 1967// TI - Error bounds for convolutional codes and an asymptotically optimum decoding algorithm JO - Inf Theory, IEEE Trans VL - 13 UR - https://doi.org/10.1109/TIT.1967.1054010 DO - 10.1109/TIT.1967.1054010 ID - Viterbi1967 ER - TY - JOUR AU - Paten, B. AU - Herrero, J. AU - Fitzgerald, S. AU - Beal, K. AU - Flicek, P. AU - Holmes, I. AU - Birney, E. PY - 2008 DA - 2008// TI - Genome-wide nucleotide-level mammalian ancestor reconstruction JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.076521.108 DO - 10.1101/gr.076521.108 ID - Paten2008 ER - TY - JOUR AU - Grasso, C. AU - Lee, C. PY - 2004 DA - 2004// TI - Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth126 DO - 10.1093/bioinformatics/bth126 ID - Grasso2004 ER - TY - JOUR AU - Thompson, J. D. AU - Koehl, P. AU - Ripp, R. AU - Poch, O. PY - 2005 DA - 2005// TI - BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark JO - Proteins: Struct, Funct, Bioinf VL - 61 UR - https://doi.org/10.1002/prot.20527 DO - 10.1002/prot.20527 ID - Thompson2005 ER - TY - JOUR AU - Gonnet, G. H. AU - Hallett, M. T. AU - Korostensky, C. AU - Bernardin, L. PY - 2000 DA - 2000// TI - Darwin v. 2.0: an interpreted computer language for the biosciences JO - Bioinformatics VL - 16 UR - https://doi.org/10.1093/bioinformatics/16.2.101 DO - 10.1093/bioinformatics/16.2.101 ID - Gonnet2000 ER - TY - JOUR AU - Benner, S. A. AU - Cohen, M. A. AU - Gonnet, G. H. PY - 1993 DA - 1993// TI - Empirical and Structural Models for Insertions and Deletions in the Divergent Evolution of Proteins JO - J Mol Biol VL - 229 UR - https://doi.org/10.1006/jmbi.1993.1105 DO - 10.1006/jmbi.1993.1105 ID - Benner1993 ER - TY - JOUR AU - Pascarella, S. AU - Argos, P. PY - 1992 DA - 1992// TI - Analysis of insertions/deletions in protein structures JO - J Mol Biol VL - 224 UR - https://doi.org/10.1016/0022-2836(92)91008-D DO - 10.1016/0022-2836(92)91008-D ID - Pascarella1992 ER - TY - BOOK AU - Durbin, R. PY - 1998 DA - 1998// TI - Biol Sequence Anal: Probabilistic Models Proteins Nucleic Acids PB - Cambridge University Press CY - Cambridge, UK UR - https://doi.org/10.1017/CBO9780511790492 DO - 10.1017/CBO9780511790492 ID - Durbin1998 ER - TY - JOUR AU - Gonnet, G. H. AU - Benner, S. A. PY - 1996 DA - 1996// TI - Probabilistic ancestral sequences and multiple alignments JO - Algorithm Theory—SWAT'96 VL - 1097/1996 UR - https://doi.org/10.1007/3-540-61422-2_147 DO - 10.1007/3-540-61422-2_147 ID - Gonnet1996 ER - TY - JOUR AU - Gonnet, G. AU - Cohen, M. AU - Benner, S. PY - 1992 DA - 1992// TI - Exhaustive matching of the entire protein sequence database JO - Science VL - 256 UR - https://doi.org/10.1126/science.1604319 DO - 10.1126/science.1604319 ID - Gonnet1992 ER - TY - JOUR AU - Whelan, S. AU - Goldman, N. PY - 2001 DA - 2001// TI - A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003851 DO - 10.1093/oxfordjournals.molbev.a003851 ID - Whelan2001 ER - TY - JOUR AU - Felsenstein, J. PY - 1981 DA - 1981// TI - Evolutionary trees from DNA sequences: A maximum likelihood approach JO - J Mol Evol VL - 17 UR - https://doi.org/10.1007/BF01734359 DO - 10.1007/BF01734359 ID - Felsenstein1981 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - BOOK AU - Kimura, M. PY - 1985 DA - 1985// TI - Neutral Theory Mol Evol PB - Cambridge University Press CY - Cambridge, UK ID - Kimura1985 ER - TY - JOUR AU - Katoh, K. AU - Misawa, K. AU - Kuma, K. i. AU - Miyata, T. PY - 2002 DA - 2002// TI - MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/gkf436 DO - 10.1093/nar/gkf436 ID - Katoh2002 ER - TY - JOUR AU - Thompson, J. D. AU - Higgins, D. G. AU - Gibson, T. J. AU - CLUSTAL, W. PY - 1994 DA - 1994// TI - Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice JO - Nucl Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - JOUR AU - Dessimoz, C. AU - Gil, M. PY - 2010 DA - 2010// TI - Phylogenetic assessment of alignments reveals neglected tree signal in gaps JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-4-r37 DO - 10.1186/gb-2010-11-4-r37 ID - Dessimoz2010 ER - TY - BOOK AU - Dalquen, D. A. AU - Anisimova, M. AU - Gonnet, G. H. AU - Dessimoz, C. PY - 2011 DA - 2011// TI - ALF—A Simulation Framework for Genome Evolution ID - Dalquen2011 ER - TY - JOUR AU - Sauder, J. M. AU - Arthur, J. W. AU - Dunbrack, R. L. PY - 2000 DA - 2000// TI - Largescale comparison of protein sequence alignment algorithms with structure alignments JO - Proteins: Struct, Func, Bioinf VL - 40 UR - https://doi.org/3.0.CO;2-7 DO - 3.0.CO;2-7 ID - Sauder2000 ER - TY - JOUR AU - Löytynoja, A. AU - Goldman, N. PY - 2008 DA - 2008// TI - Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis JO - Science VL - 320 UR - https://doi.org/10.1126/science.1158395 DO - 10.1126/science.1158395 ID - Löytynoja2008 ER - TY - JOUR AU - Altenhoff, A. M. AU - Schneider, A. AU - Gonnet, G. H. AU - Dessimoz, C. PY - 2010 DA - 2010// TI - OMA 2011: orthology inference among 1000 complete genomes JO - Nucleic Acids Res VL - 39 ID - Altenhoff2010 ER - TY - JOUR AU - Robinson, D. AU - Foulds, L. PY - 1981 DA - 1981// TI - Comparison of phylogenetic trees JO - Math Biosci VL - 53 UR - https://doi.org/10.1016/0025-5564(81)90043-2 DO - 10.1016/0025-5564(81)90043-2 ID - Robinson1981 ER -