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Items: 1 to 20 of 116

1.

Agalma: an automated phylogenomics workflow.

Dunn CW, Howison M, Zapata F.

BMC Bioinformatics. 2013 Nov 19;14:330. doi: 10.1186/1471-2105-14-330.

2.

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.

Schreiber F, Pick K, Erpenbeck D, Wörheide G, Morgenstern B.

BMC Bioinformatics. 2009 Jul 16;10:219. doi: 10.1186/1471-2105-10-219.

3.
4.

Phylogenomics Using Transcriptome Data.

Cannon JT, Kocot KM.

Methods Mol Biol. 2016;1452:65-80. doi: 10.1007/978-1-4939-3774-5_4.

PMID:
27460370
5.

phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics.

Guy L.

Bioinformatics. 2017 Apr 15;33(8):1230-1232. doi: 10.1093/bioinformatics/btw824.

6.

BaCoCa--a heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions.

Kück P, Struck TH.

Mol Phylogenet Evol. 2014 Jan;70:94-8. doi: 10.1016/j.ympev.2013.09.011. Epub 2013 Sep 25.

PMID:
24076250
7.

Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.

Tzika AC, Ullate-Agote A, Grbic D, Milinkovitch MC.

Genome Biol Evol. 2015 Jul 1;7(6):1827-41. doi: 10.1093/gbe/evv106.

8.

HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching.

Bi G, Mao Y, Xing Q, Cao M.

Genomics. 2018 Jan;110(1):18-22. doi: 10.1016/j.ygeno.2017.08.001. Epub 2017 Aug 3.

9.

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.

Speiser DI, Pankey MS, Zaharoff AK, Battelle BA, Bracken-Grissom HD, Breinholt JW, Bybee SM, Cronin TW, Garm A, Lindgren AR, Patel NH, Porter ML, Protas ME, Rivera AS, Serb JM, Zigler KS, Crandall KA, Oakley TH.

BMC Bioinformatics. 2014 Nov 19;15:350. doi: 10.1186/s12859-014-0350-x.

10.

Phylogenomics from Whole Genome Sequences Using aTRAM.

Allen JM, Boyd B, Nguyen NP, Vachaspati P, Warnow T, Huang DI, Grady PGS, Bell KC, Cronk QCB, Mugisha L, Pittendrigh BR, Leonardi MS, Reed DL, Johnson KP.

Syst Biol. 2017 Sep 1;66(5):786-798. doi: 10.1093/sysbio/syw105.

PMID:
28123117
11.

OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis.

Rago A, Gilbert DG, Choi JH, Sackton TB, Wang X, Kelkar YD, Werren JH, Colbourne JK.

BMC Genomics. 2016 Aug 25;17:678. doi: 10.1186/s12864-016-2886-9.

12.

GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes.

Chen X, Wang Y, Sheng Y, Warren A, Gao S.

Mol Ecol Resour. 2018 May;18(3):700-713. doi: 10.1111/1755-0998.12750. Epub 2018 Feb 8.

PMID:
29314766
13.
14.

PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R.

Dornburg A, Fisk JN, Tamagnan J, Townsend JP.

BMC Evol Biol. 2016 Dec 1;16(1):262.

15.

SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics.

Roure B, Rodriguez-Ezpeleta N, Philippe H.

BMC Evol Biol. 2007 Feb 8;7 Suppl 1:S2.

16.

PhyloGena--a user-friendly system for automated phylogenetic annotation of unknown sequences.

Hanekamp K, Bohnebeck U, Beszteri B, Valentin K.

Bioinformatics. 2007 Apr 1;23(7):793-801. Epub 2007 Mar 1.

PMID:
17332025
17.

Anvaya: a workflows environment for automated genome analysis.

Limaye B, Banerjee R, Datta A, Inamdar H, Vats P, Dahale S, Bhandari A, Ramakrishnan EP, Tupakula R, Malviya S, Bayaskar A, Gadhari R, Jain S, Gavane V, Mahajan R, Sunitha K, Joshi R.

J Bioinform Comput Biol. 2012 Aug;10(4):1250006. doi: 10.1142/S0219720012500060. Epub 2012 Jun 22.

PMID:
22809419
18.

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta).

Parks MB, Wickett NJ, Alverson AJ.

Mol Biol Evol. 2018 Jan 1;35(1):80-93. doi: 10.1093/molbev/msx268.

19.

Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system.

Oakley TH, Alexandrou MA, Ngo R, Pankey MS, Churchill CK, Chen W, Lopker KB.

BMC Bioinformatics. 2014 Jul 2;15:230. doi: 10.1186/1471-2105-15-230.

20.

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