@article {Edgar2004,
	title = {{MUSCLE: multiple sequence alignment with high accuracy and high throughput.}},
	journal = {Nucleic acids research},
	volume = {32},
	number = {5},
	year = {2004},
	pages = {1792{\textendash}7},
	abstract = {We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.},
	keywords = {Algorithms, Amino Acid Motifs, Amino Acid Sequence, Internet, Molecular Sequence Data, Protein, Protein: methods, Reproducibility of Results, Sequence Alignment, Sequence Alignment: methods, Sequence Analysis, Software, Time Factors},
	issn = {1362-4962},
	doi = {10.1093/nar/gkh340},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=390337\&tool=pmcentrez\&rendertype=abstract},
	author = {Edgar, Robert C}
}
@article {Stephens2005,
	title = {{Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation.}},
	journal = {American journal of human genetics},
	volume = {76},
	number = {3},
	year = {2005},
	pages = {449{\textendash}62},
	abstract = {Although many algorithms exist for estimating haplotypes from genotype data, none of them take full account of both the decay of linkage disequilibrium (LD) with distance and the order and spacing of genotyped markers. Here, we describe an algorithm that does take these factors into account, using a flexible model for the decay of LD with distance that can handle both "blocklike" and "nonblocklike" patterns of LD. We compare the accuracy of this approach with a range of other available algorithms in three ways: for reconstruction of randomly paired, molecularly determined male X chromosome haplotypes; for reconstruction of haplotypes obtained from trios in an autosomal region; and for estimation of missing genotypes in 50 autosomal genes that have been completely resequenced in 24 African Americans and 23 individuals of European descent. For the autosomal data sets, our new approach clearly outperforms the best available methods, whereas its accuracy in inferring the X chromosome haplotypes is only slightly superior. For estimation of missing genotypes, our method performed slightly better when the two subsamples were combined than when they were analyzed separately, which illustrates its robustness to population stratification. Our method is implemented in the software package PHASE (v2.1.1), available from the Stephens Lab Web site.},
	keywords = {Algorithms, Alleles, Biometry, Chromosomes, Data Interpretation, Genetic, Genomics, Genomics: statistics \& numerical data, Genotype, Haplotypes, Haplotypes: genetics, Human, Humans, Linkage Disequilibrium, Male, Models, Software, Statistical, X, X: genetics},
	issn = {0002-9297},
	doi = {10.1086/428594},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1196397\&tool=pmcentrez\&rendertype=abstract},
	author = {Stephens, Matthew and Scheet, Paul}
}
