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Items: 1 to 20 of 131

1.

CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes.

Cheng J, Zeng X, Ren G, Liu Z.

BMC Bioinformatics. 2013 Mar 14;14:95. doi: 10.1186/1471-2105-14-95.

2.

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.

Liu C, Shi L, Zhu Y, Chen H, Zhang J, Lin X, Guan X.

BMC Genomics. 2012 Dec 20;13:715. doi: 10.1186/1471-2164-13-715.

3.

Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes.

McKain MR, Hartsock RH, Wohl MM, Kellogg EA.

Bioinformatics. 2017 Jan 1;33(1):130-132. doi: 10.1093/bioinformatics/btw583. Epub 2016 Sep 14.

4.

AGP: a multimethods web server for alignment-free genome phylogeny.

Cheng J, Cao F, Liu Z.

Mol Biol Evol. 2013 May;30(5):1032-7. doi: 10.1093/molbev/mst021. Epub 2013 Feb 6.

PMID:
23389766
5.
6.

ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection.

Sablok G, Padma Raju GV, Mudunuri SB, Prabha R, Singh DP, Baev V, Yahubyan G, Ralph PJ, La Porta N.

Database (Oxford). 2015 Sep 27;2015. pii: bav084. doi: 10.1093/database/bav084. Print 2015.

7.

Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes.

Gao L, Yi X, Yang YX, Su YJ, Wang T.

BMC Evol Biol. 2009 Jun 11;9:130. doi: 10.1186/1471-2148-9-130.

8.

Analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes: origin and evolution of allotetraploids.

Xu Q, Xiong G, Li P, He F, Huang Y, Wang K, Li Z, Hua J.

PLoS One. 2012;7(8):e37128. doi: 10.1371/journal.pone.0037128. Epub 2012 Aug 2. Erratum in: PLoS One. 2013;8(5). doi: 10.1371/annotation/47563c17-536c-465d-9b93-cd35a78f6e66.

9.

Complete chloroplast genome sequences of Mongolia medicine Artemisia frigida and phylogenetic relationships with other plants.

Liu Y, Huo N, Dong L, Wang Y, Zhang S, Young HA, Feng X, Gu YQ.

PLoS One. 2013;8(2):e57533. doi: 10.1371/journal.pone.0057533. Epub 2013 Feb 27.

10.

High-accuracy de novo assembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy.

Li Q, Li Y, Song J, Xu H, Xu J, Zhu Y, Li X, Gao H, Dong L, Qian J, Sun C, Chen S.

New Phytol. 2014 Dec;204(4):1041-9. doi: 10.1111/nph.12966. Epub 2014 Aug 8.

11.

Complete chloroplast genome sequences of Praxelis (Eupatorium catarium Veldkamp), an important invasive species.

Zhang Y, Li L, Yan TL, Liu Q.

Gene. 2014 Oct 1;549(1):58-69. doi: 10.1016/j.gene.2014.07.041. Epub 2014 Jul 15.

PMID:
25042453
12.
13.

CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes.

Xu Z, Hao B.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W174-8. doi: 10.1093/nar/gkp278. Epub 2009 Apr 26.

14.

Chloroplast genome analysis of Australian eucalypts--Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae).

Bayly MJ, Rigault P, Spokevicius A, Ladiges PY, Ades PK, Anderson C, Bossinger G, Merchant A, Udovicic F, Woodrow IE, Tibbits J.

Mol Phylogenet Evol. 2013 Dec;69(3):704-16. doi: 10.1016/j.ympev.2013.07.006. Epub 2013 Jul 19.

PMID:
23876290
15.

SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.

Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F.

PLoS One. 2012;7(10):e48053. doi: 10.1371/journal.pone.0048053. Epub 2012 Oct 24.

16.

Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses.

Ma PF, Guo ZH, Li DZ.

PLoS One. 2012;7(1):e30297. doi: 10.1371/journal.pone.0030297. Epub 2012 Jan 17.

17.
18.

Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale -a wild ancestor of cultivated buckwheat.

Logacheva MD, Samigullin TH, Dhingra A, Penin AA.

BMC Plant Biol. 2008 May 20;8:59. doi: 10.1186/1471-2229-8-59.

19.

Methods for obtaining and analyzing whole chloroplast genome sequences.

Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl JV, McNeal JR, Leebens-Mack J, Cui L.

Methods Enzymol. 2005;395:348-84.

PMID:
15865976
20.

MicroScope: a platform for microbial genome annotation and comparative genomics.

Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, M├ędigue C.

Database (Oxford). 2009;2009:bap021. Epub 2009 Nov 25.

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