Research references

Darling AE, Mau B, and Perna NT (2010). “progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss, and Rearrangement.” PLoS One. 5(6):e11147. (See the PLOS ONE entry.)

Dayhoff MO, Schwartz R and Orcutt BC (1978). “A model of evolutionary change in proteins”. Atlas of protein sequence and structure (volume 5, supplement 3 ed.). Nat. Biomed. Res. Found. pp. 345–358. ISBN 0-912466-07-3.

Edgar RC (2004). “MUSCLE: multiple sequence alignment with high accuracy and high throughput.” Nucleic Acids Res. 32(5):1792-1797. (See the PubMed entry).

Edgar RC (2004). “MUSCLE: a multiple sequence alignment method with reduced time and space complexity.” BMC Bioinformatics (5):113 (See the PubMed entry).

Gascuel O (1997). “ BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.” Molecular Biology and Evolution 14:685-695. (See the PubMed entry.) [[MegAlign Pro’s tree-building algorithm]

Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD and Bairoch A (2005). "Protein Identification and Analysis Tools on the ExPASy Server." In The Proteomics Protocols Handbook, ed. John M. Walker, Humana Press, pp. 571-607.

Guruprasad K, Reddy BVB and Pandit MW (1990). "Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence." Protein Eng., 4, 155 – 161.
Henikoff S & Henikoff JG (1992). “Amino Acid Substitution Matrices from Protein Blocks”. PNAS. 89 (22): 10915–10919. (See the PubMed entry)

Katoh M, Kumar M (2002) “MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.” (Nucleic Acids Res. 30:3059-3066).

Kimura M (1980). “A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.” J. Mol. Evol., 16: 111-120.

Kimura M (1983). The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.

Kyte J, Doolittle RF. (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol., 157, 105-132. [Hydrophobicity color scheme ]

Lehninger A (2005). Principles of Biochemistry, 4th Edition, Chapter 3, page 78, Table 3-1.

Lehninger A, Nelson D, and Cox M (2005). “Principles of biochemistry.” New York: W.H. Freeman.

Müller T, Spang R, Vingron M (2002). “Estimating amino acid substitution models: a comparison of Dayhoff’s estimator, the resolvent approach and a maximum likelihood method.” Mol Biol Evol. 2002 Jan;19(1):8-13. (See the PubMed entry)

Müller T & Vingron (2000). “Modeling amino acid replacement.” J Comput Biol. 2000;7(6):761-76. (See the PubMed entry)

Nishino, Kunihiko & Yamasaki, Seiji & Hayashi-Nishino, Mitsuko & Yamaguchi, Akihito. (2010). “Effect of NlpE Overproduction on Multidrug Resistance in Escherichia coli.” Antimicrobial agents and chemotherapy. 54. 2239-43. 10.1128/AAC.01677-09. [ View on PubMed ]

Saito N and Nei M (1987). “The neighbor-joining method: a new method for reconstructing phylogenetic trees.” Mol Biol Evol. 1987 Jul;4(4):406-25.

Schneider TD and Stephens RM (1990). “Sequence logos: a new way to display consensus sequences.” Nucleic Acids Research, 18 (20): 6097-6100 doi:10.1093/nar/18.20.6097. (See the PubMed entry) [Sequence Logo track]

Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins D (2011). “Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.” Molecular Systems Biology 7, Article number: 539 (See the article in Nature)

Sonnhammer ELL and Hollich V (2005). “Scoredist: A simple and robust protein sequence distance estimator.” BMC Bioinformatics 2005, 6:108. (See on Biomed Central.) [Scoredist model]

Stamatakis A (2014). “RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies”. Bioinformatics, 2014. [RAxML tree-building algorithm]

Tamura K and Nei M (1993). “Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.” Mol Biol Evol. 1993 May;10(3):512-26.

Taylor WR (1997). “Residual colours: a proposal for aminochromography.” Protein Engineering vol.10 no.7 pp.743 – 746. (See the PDF file.) [Taylor color scheme ]

Thompson JD, Higgins DG and Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22:4673-4680. [Clustal X color scheme ]

Thorne JL, Kishino H, Painter IS (December, 1998). “Estimating the rate of evolution of the rate of molecular evolution”. Mol. Biol. Evol. 15 (12): 1647–57. (See the PubMed entry the PubMed entry)

Waterhouse AM, Procter JB, Martin DMA, Clamp M and Barton GJ (2009). “JalView version 2: a multiple sequence alignment and analysis workbench.” Bioinformatics 25:1189 – 1191. (See on PMC.) [Discusses methodology later used to create the Taylor and Zappo color schemes ]