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Items: 1 to 20 of 97

1.

ALF--a simulation framework for genome evolution.

Dalquen DA, Anisimova M, Gonnet GH, Dessimoz C.

Mol Biol Evol. 2012 Apr;29(4):1115-23. doi: 10.1093/molbev/msr268. Epub 2011 Dec 8.

3.

GENOMEPOP: a program to simulate genomes in populations.

Carvajal-Rodríguez A.

BMC Bioinformatics. 2008 Apr 30;9:223. doi: 10.1186/1471-2105-9-223.

4.

MSOAR: a high-throughput ortholog assignment system based on genome rearrangement.

Fu Z, Chen X, Vacic V, Nan P, Zhong Y, Jiang T.

J Comput Biol. 2007 Nov;14(9):1160-75.

PMID:
17990975
5.

INDELible: a flexible simulator of biological sequence evolution.

Fletcher W, Yang Z.

Mol Biol Evol. 2009 Aug;26(8):1879-88. doi: 10.1093/molbev/msp098. Epub 2009 May 7.

6.

Inferring horizontal gene transfer.

Ravenhall M, Škunca N, Lassalle F, Dessimoz C.

PLoS Comput Biol. 2015 May 28;11(5):e1004095. doi: 10.1371/journal.pcbi.1004095. eCollection 2015 May.

7.

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.

8.

CodonExplorer: an interactive online database for the analysis of codon usage and sequence composition.

Zaneveld J, Hamady M, Sueoka N, Knight R.

Methods Mol Biol. 2009;537:207-32. doi: 10.1007/978-1-59745-251-9_10.

9.

An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes.

Stern A, Mayrose I, Penn O, Shaul S, Gophna U, Pupko T.

Syst Biol. 2010 Mar;59(2):212-25. doi: 10.1093/sysbio/syp104. Epub 2010 Jan 15.

10.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

11.

CodonO: codon usage bias analysis within and across genomes.

Angellotti MC, Bhuiyan SB, Chen G, Wan XF.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W132-6. Epub 2007 May 30.

12.

MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.

Cai JJ, Smith DK, Xia X, Yuen KY.

BMC Bioinformatics. 2005 Mar 22;6:64.

13.

FGF: a web tool for Fishing Gene Family in a whole genome database.

Zheng H, Shi J, Fang X, Li Y, Vang S, Fan W, Wang J, Zhang Z, Wang W, Kristiansen K, Wang J.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W121-5. Epub 2007 Jun 21.

14.

Simulating DNA coding sequence evolution with EvolveAGene 3.

Hall BG.

Mol Biol Evol. 2008 Apr;25(4):688-95. doi: 10.1093/molbev/msn008. Epub 2008 Jan 12.

PMID:
18192698
15.

indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels.

Strope CL, Scott SD, Moriyama EN.

Mol Biol Evol. 2007 Mar;24(3):640-9. Epub 2006 Dec 8.

PMID:
17158778
16.

Probabilistic phylogenetic inference with insertions and deletions.

Rivas E, Eddy SR.

PLoS Comput Biol. 2008 Sep 19;4(9):e1000172. doi: 10.1371/journal.pcbi.1000172.

17.

Vestige: maximum likelihood phylogenetic footprinting.

Wakefield MJ, Maxwell P, Huttley GA.

BMC Bioinformatics. 2005 May 29;6:130.

18.

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs.

Dutheil J, Boussau B.

BMC Evol Biol. 2008 Sep 22;8:255. doi: 10.1186/1471-2148-8-255.

19.

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.

Bansal MS, Alm EJ, Kellis M.

Bioinformatics. 2012 Jun 15;28(12):i283-91. doi: 10.1093/bioinformatics/bts225.

20.

Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples.

Tuller T, Birin H, Kupiec M, Ruppin E.

J Comput Biol. 2010 Sep;17(9):1327-44. doi: 10.1089/cmb.2010.0112.

PMID:
20874411

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