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Items: 1 to 20 of 102

1.

Estimating population diversity with CatchAll.

Bunge J, Woodard L, Böhning D, Foster JA, Connolly S, Allen HK.

Bioinformatics. 2012 Apr 1;28(7):1045-7. doi: 10.1093/bioinformatics/bts075. Epub 2012 Feb 13.

2.

Estimating the number of species with CatchAll.

Bunge J.

Pac Symp Biocomput. 2011:121-30.

3.

A fast and reliable computational method for estimating population genetic parameters.

Vasco DA.

Genetics. 2008 Jun;179(2):951-63. doi: 10.1534/genetics.108.087049. Epub 2008 May 27.

4.

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.

Stamatakis A, Ludwig T, Meier H.

Bioinformatics. 2005 Feb 15;21(4):456-63. Epub 2004 Dec 17.

PMID:
15608047
5.

Fast and efficient estimation of individual ancestry coefficients.

Frichot E, Mathieu F, Trouillon T, Bouchard G, François O.

Genetics. 2014 Apr;196(4):973-83. doi: 10.1534/genetics.113.160572. Epub 2014 Feb 4.

6.

Computationally Efficient Composite Likelihood Statistics for Demographic Inference.

Coffman AJ, Hsieh PH, Gravel S, Gutenkunst RN.

Mol Biol Evol. 2016 Feb;33(2):591-3. doi: 10.1093/molbev/msv255. Epub 2015 Nov 5.

PMID:
26545922
8.

CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data.

Fidaner IB, Cankorur-Cetinkaya A, Dikicioglu D, Kirdar B, Cemgil AT, Oliver SG.

Bioinformatics. 2016 Feb 1;32(3):388-97. doi: 10.1093/bioinformatics/btv532. Epub 2015 Sep 26.

9.

Estimation of viral richness from shotgun metagenomes using a frequency count approach.

Allen HK, Bunge J, Foster JA, Bayles DO, Stanton TB.

Microbiome. 2013 Feb 4;1(1):5. doi: 10.1186/2049-2618-1-5.

10.

Advanced complex trait analysis.

Gray A, Stewart I, Tenesa A.

Bioinformatics. 2012 Dec 1;28(23):3134-6. doi: 10.1093/bioinformatics/bts571. Epub 2012 Sep 27.

PMID:
23023980
11.

MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.

Mol Biol Evol. 2011 Oct;28(10):2731-9. doi: 10.1093/molbev/msr121. Epub 2011 May 4.

12.

OpenStructure: a flexible software framework for computational structural biology.

Biasini M, Mariani V, Haas J, Scheuber S, Schenk AD, Schwede T, Philippsen A.

Bioinformatics. 2010 Oct 15;26(20):2626-8. doi: 10.1093/bioinformatics/btq481. Epub 2010 Aug 23.

13.

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations.

Corander J, Marttinen P, Sirén J, Tang J.

BMC Bioinformatics. 2008 Dec 16;9:539. doi: 10.1186/1471-2105-9-539.

14.

Efficient simulation and likelihood methods for non-neutral multi-allele models.

Joyce P, Genz A, Buzbas EO.

J Comput Biol. 2012 Jun;19(6):650-61. doi: 10.1089/cmb.2012.0033.

15.

OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing.

Das S, Vikalo H.

Bioinformatics. 2012 Jul 1;28(13):1677-83. doi: 10.1093/bioinformatics/bts256. Epub 2012 May 7.

16.

Calibrating E-values for hidden Markov models using reverse-sequence null models.

Karplus K, Karchin R, Shackelford G, Hughey R.

Bioinformatics. 2005 Nov 15;21(22):4107-15. Epub 2005 Aug 25.

PMID:
16123115
17.

ANGSD: Analysis of Next Generation Sequencing Data.

Korneliussen TS, Albrechtsen A, Nielsen R.

BMC Bioinformatics. 2014 Nov 25;15:356. doi: 10.1186/s12859-014-0356-4.

18.

Comparison of Bayesian and maximum-likelihood inference of population genetic parameters.

Beerli P.

Bioinformatics. 2006 Feb 1;22(3):341-5. Epub 2005 Nov 29.

PMID:
16317072
19.

PopABC: a program to infer historical demographic parameters.

Lopes JS, Balding D, Beaumont MA.

Bioinformatics. 2009 Oct 15;25(20):2747-9. doi: 10.1093/bioinformatics/btp487. Epub 2009 Aug 13.

PMID:
19679678
20.

Blockwise HMM computation for large-scale population genomic inference.

Paul JS, Song YS.

Bioinformatics. 2012 Aug 1;28(15):2008-15. doi: 10.1093/bioinformatics/bts314. Epub 2012 May 28.

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