TY - JOUR AU - Renner, S. S. PY - 2014 DA - 2014// TI - The relative and absolute frequencies of angiosperm sexual systems: Dioecy, monoecy, gynodioecy, and an updated online database JO - Am J Bot VL - 101 UR - https://doi.org/10.3732/ajb.1400196 DO - 10.3732/ajb.1400196 ID - Renner2014 ER - TY - JOUR AU - Hanson, M. R. AU - Bentolila, S. PY - 2004 DA - 2004// TI - Interactions of mitochondrial and nuclear genes that affect male gametophyte development JO - Plant Cell VL - 16 UR - https://doi.org/10.1105/tpc.015966 DO - 10.1105/tpc.015966 ID - Hanson2004 ER - TY - JOUR AU - Kazama, T. PY - 2008 DA - 2008// TI - Nakamura, Watanabe, M. Sugita KT. Suppression mechanism of mitochondrial ORF79 accumulation by Rf1 protein in BT-type cytoplasmic male sterile rice JO - Plant J VL - 55 UR - https://doi.org/10.1111/j.1365-313X.2008.03529.x DO - 10.1111/j.1365-313X.2008.03529.x ID - Kazama2008 ER - TY - JOUR AU - Wang, K. AU - Gao, F. AU - Ji, Y. AU - Liu, Y. AU - Dan, Z. AU - Yang, P. PY - 2013 DA - 2013// TI - ORFH79 impairs mitochondrial function via interaction with a subunit of electron transport chain complex III in Honglian cytoplasmic male sterile rice JO - New Phytol VL - 198 UR - https://doi.org/10.1111/nph.12180 DO - 10.1111/nph.12180 ID - Wang2013 ER - TY - JOUR AU - Sabar, M. AU - Gagliardi, D. AU - Balk, J. AU - Leaver, C. PY - 2003 DA - 2003// TI - ORFB is a subunit of F1FO-ATP synthase: insight into the basis of cytoplasmic male sterility in sunflower JO - EMBO Rep VL - 4 UR - https://doi.org/10.1038/sj.embor.embor800 DO - 10.1038/sj.embor.embor800 ID - Sabar2003 ER - TY - JOUR AU - Allen, J. O. AU - Fauron, C. M. AU - Minx, P. AU - Roark, L. AU - Oddiraju, S. AU - Guan, N. L. PY - 2007 DA - 2007// TI - Comparisons among two fertile and three male-sterile mitochondrial genomes of maize JO - Genetics VL - 177 UR - https://doi.org/10.1534/genetics.107.073312 DO - 10.1534/genetics.107.073312 ID - Allen2007 ER - TY - JOUR AU - Darracq, A. AU - Varré, J. S. AU - Maréchal-Drouard, L. AU - Courseaux, A. AU - Castric, V. AU - Saumitou-Laprade, P. PY - 2011 DA - 2011// TI - Structural and content diversity of mitochondrial genome in beet: a comparative genomic analysis JO - Genome Biol Evol VL - 3 UR - https://doi.org/10.1093/gbe/evr042 DO - 10.1093/gbe/evr042 ID - Darracq2011 ER - TY - JOUR AU - Charlesworth, D. AU - Laporte, V. PY - 1998 DA - 1998// TI - The male-sterility polymorphism of Silene vulgaris: analysis of genetic data: from two populations and comparison with Thymus vulgaris JO - Genetics VL - 150 ID - Charlesworth1998 ER - TY - JOUR AU - Desfeux, C. AU - Maurice, S. AU - Henry, J. P. AU - Lejeune, B. AU - Gouyon, P. H. PY - 1996 DA - 1996// TI - Reproductive Systems in the Genus Silene. Evolution of reproductive systems in the genus Silene JO - Proc R Soc B Biol Sci VL - 263 UR - https://doi.org/10.1098/rspb.1996.0062 DO - 10.1098/rspb.1996.0062 ID - Desfeux1996 ER - TY - STD TI - Casimiro-Soriguer I, Buide ML, Narbona E. Diversity of sexual systems within different lineages of the genus Silene. AOB Plants. 2015;7:plv037. doi:https://doi.org/10.1093/aobpla/plv037 ID - ref10 ER - TY - JOUR AU - Städler, T. AU - Delph, L. F. PY - 2002 DA - 2002// TI - Ancient mitochondrial haplotypes and evidence for intragenic recombination in a gynodioecious plant JO - Proc Natl Acad Sci U S A VL - 99 UR - https://doi.org/10.1073/pnas.182267799 DO - 10.1073/pnas.182267799 ID - Städler2002 ER - TY - JOUR AU - Touzet, P. AU - Delph, L. F. PY - 2009 DA - 2009// TI - The effect of breeding system on polymorphism in mitochondrial genes of silene JO - Genetics. VL - 181 UR - https://doi.org/10.1534/genetics.108.092411 DO - 10.1534/genetics.108.092411 ID - Touzet2009 ER - TY - JOUR AU - Mower, J. P. AU - Touzet, P. AU - Gummow, J. S. AU - Delph, L. F. AU - Palmer, J. D. PY - 2007 DA - 2007// TI - Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants JO - BMC Evol Biol VL - 7 UR - https://doi.org/10.1186/1471-2148-7-135 DO - 10.1186/1471-2148-7-135 ID - Mower2007 ER - TY - STD TI - Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, et al. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol. 2012;10: e1001241. doi:0.1371/journal.pbio.1001241. UR - https://doi.org/0.1371/journal.pbio.1001241 ID - ref14 ER - TY - JOUR AU - Sloan, D. B. AU - Alverson, A. J. AU - Wu, M. AU - Palmer, J. D. AU - Taylor, D. R. PY - 2012 DA - 2012// TI - Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus Silene JO - Genome Biol Evol. VL - 4 UR - https://doi.org/10.1093/gbe/evs006 DO - 10.1093/gbe/evs006 ID - Sloan2012 ER - TY - JOUR AU - Sloan, D. B. AU - Müller, K. AU - McCauley, D. E. AU - Taylor, D. R. AU - Storchová, H. PY - 2012 DA - 2012// TI - Intraspecific variation in mitochondrial genome sequence, structure, and gene content in Silene vulgaris, an angiosperm with pervasive cytoplasmic male sterility JO - New Phytol VL - 196 UR - https://doi.org/10.1111/j.1469-8137.2012.04340.x DO - 10.1111/j.1469-8137.2012.04340.x ID - Sloan2012 ER - TY - JOUR AU - Sloan, D. B. AU - Triant, D. A. AU - Forrester, N. J. AU - Bergner, L. M. AU - Wu, M. AU - Taylor, D. R. PY - 2014 DA - 2014// TI - A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae) JO - Mol Phylogenet Evol VL - 72 UR - https://doi.org/10.1016/j.ympev.2013.12.004 DO - 10.1016/j.ympev.2013.12.004 ID - Sloan2014 ER - TY - JOUR AU - Štorchová, H. AU - Stone, J. D. AU - Sloan, D. B. AU - Abeyawardana, O. A. J. AU - Muller, K. AU - Walterová, J. AU - Pažoutová, M. PY - 2018 DA - 2018// TI - Homologous recombination changes the context of cytochrome b transcription in the mitochondrial genome of Silene vulgaris KRA JO - BMC Genomics VL - 19 UR - https://doi.org/10.1186/s12864-018-5254-0 DO - 10.1186/s12864-018-5254-0 ID - Štorchová2018 ER - TY - JOUR AU - Stone, J. D. AU - Koloušková, P. AU - Sloan, D. B. AU - Štorchová, H. PY - 2017 DA - 2017// TI - Non-coding RNA may be associated with cytoplasmic male sterility in Silene vulgaris JO - J Exp Bot VL - 68 UR - https://doi.org/10.1093/jxb/erx057 DO - 10.1093/jxb/erx057 ID - Stone2017 ER - TY - JOUR AU - Abbate, J. L. AU - Antonovics, J. PY - 2014 DA - 2014// TI - Elevational disease distribution in a natural plant–pathogen system: insights from changes across host populations and climate JO - Oikos VL - 123 UR - https://doi.org/10.1111/oik.01001 DO - 10.1111/oik.01001 ID - Abbate2014 ER - TY - JOUR AU - Li, Z. F. AU - Zhang, Y. C. AU - Chen, Y. Q. PY - 2015 DA - 2015// TI - MiRNAs and lncRNAs in reproductive development JO - Plant Sci VL - 238 UR - https://doi.org/10.1016/j.plantsci.2015.05.017 DO - 10.1016/j.plantsci.2015.05.017 ID - Li2015 ER - TY - JOUR AU - Wu, J. AU - Zhang, M. AU - Zhang, B. AU - Zhang, X. AU - Guo, L. AU - Qi, T. PY - 2017 DA - 2017// TI - Genome-wide comparative transcriptome analysis of CMS-D2 and its maintainer and restorer lines in upland cotton JO - BMC Genomics VL - 18 UR - https://doi.org/10.1186/s12864-017-3841-0 DO - 10.1186/s12864-017-3841-0 ID - Wu2017 ER - TY - JOUR AU - Hamid, R. AU - Tomar, R. S. AU - Marashi, H. AU - Malekzadeh, S. AU - Golakiya, B. A. AU - Mohsenpour, M. PY - 2018 DA - 2018// TI - Transcriptome profiling and cataloging differential gene expression in floral buds of fertile and sterile lines of cotton (Gossypium hirsutum L.) JO - Gene VL - 660 UR - https://doi.org/10.1016/j.gene.2018.03.070 DO - 10.1016/j.gene.2018.03.070 ID - Hamid2018 ER - TY - JOUR AU - Plöchinger, M. AU - Schwenkert, S. AU - Sydow, L. AU - Schroder, W. P. AU - Meurer, J. PY - 2016 DA - 2016// TI - Functional update of the auxiliary TerC and ALB3 in maintenance and assembly of PSII JO - Front Plant Sci VL - 7 UR - https://doi.org/10.3389/fpls.2016.00423 DO - 10.3389/fpls.2016.00423 ID - Plöchinger2016 ER - TY - JOUR AU - Castandet, B. AU - Hotto, A. M. AU - Strickler, S. R. AU - Stern, D. B. PY - 2016 DA - 2016// TI - ChloroSeq, an optimized chloroplast RNA-Seq bioinformatic pipeline, reveals Remodeling of the organellar transcriptome under heat stress JO - G3-Genes Genomes Genet VL - 6 UR - https://doi.org/10.1534/g3.116.030783 DO - 10.1534/g3.116.030783 ID - Castandet2016 ER - TY - JOUR AU - Hein, A. AU - Polsakiewicz, M. AU - Knoop, V. PY - 2016 DA - 2016// TI - Frequent chloroplast RNA editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors JO - BMC Evol Biol VL - 16 UR - https://doi.org/10.1186/s12862-016-0589-0 DO - 10.1186/s12862-016-0589-0 ID - Hein2016 ER - TY - JOUR AU - Wang, W. AU - Zhang, W. AU - Wu, Y. AU - Maliga, P. AU - Messing, J. PY - 2015 DA - 2015// TI - RNA editing in chloroplasts of Spirodela polyrhiza, an aquatic monocotelydonous species JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0140285 DO - 10.1371/journal.pone.0140285 ID - Wang2015 ER - TY - JOUR AU - Wang, M. AU - Liu, H. AU - Ge, L. AU - Xing, G. AU - Wang, M. AU - Weining, S. PY - 2017 DA - 2017// TI - Identification and analysis of RNA editing sites in the chloroplast transcripts of Aegilops tauschii L JO - Genes VL - 8 UR - https://doi.org/10.3390/genes8010013 DO - 10.3390/genes8010013 ID - Wang2017 ER - TY - JOUR AU - Ruwe, H. AU - Castandet, B. AU - Schmitz-Linneweber, C. AU - Stern, D. B. PY - 2013 DA - 2013// TI - Arabidopsis chloroplast quantitative editotype JO - FEBS Lett VL - 587 UR - https://doi.org/10.1016/j.febslet.2013.03.022 DO - 10.1016/j.febslet.2013.03.022 ID - Ruwe2013 ER - TY - JOUR AU - Tangphatsornruang, S. AU - Uthaipaisanwong, P. AU - Sangsrakru, D. AU - Chanprasert, J. AU - Yoocha, T. AU - Jomchai, N. PY - 2011 DA - 2011// TI - Characterization of the complete chloroplast genome of Hevea brasiliensis reveals genome rearrangement, RNA editing sites and phylogenetic relationships JO - Gene. VL - 475 UR - https://doi.org/10.1016/j.gene.2011.01.002 DO - 10.1016/j.gene.2011.01.002 ID - Tangphatsornruang2011 ER - TY - JOUR AU - Hirose, T. AU - Kusumegi, T. AU - Tsudzuki, T. AU - Sugiura, M. PY - 1999 DA - 1999// TI - RNA editing sites in tobacco chloroplast transcripts : editing as a possible regulator of chloroplast RNA polymerase activity JO - Mol Gen Genet VL - 262 UR - https://doi.org/10.1007/s004380051106 DO - 10.1007/s004380051106 ID - Hirose1999 ER - TY - JOUR AU - Lin, C. AU - Ko, C. AU - Kuo, C. AU - Liu, M. AU - Schafleitner, R. PY - 2015 DA - 2015// TI - Transcriptional slippage and RNA editing increase the diversity of transcripts in chloroplasts : insight from deep sequencing of Vigna radiata genome and transcriptome JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0129396 DO - 10.1371/journal.pone.0129396 ID - Lin2015 ER - TY - JOUR AU - Berardi, A. E. AU - Fields, P. D. AU - Abbate, J. L. AU - Taylor, D. R. PY - 2016 DA - 2016// TI - Elevational divergence and clinal variation in floral color and leaf chemistry in Silene vulgaris JO - Am J Bot VL - 103 UR - https://doi.org/10.3732/ajb.1600106 DO - 10.3732/ajb.1600106 ID - Berardi2016 ER - TY - JOUR AU - Tseng, C. C. AU - Lee, C. J. AU - Chung, Y. T. AU - Sung, T. Y. AU - Hsieh, M. H. PY - 2013 DA - 2013// TI - Differential regulation of Arabidopsis plastid gene expression and RNA editing in non-photosynthetic tissues JO - Plant Mol Biol VL - 82 UR - https://doi.org/10.1007/s11103-013-0069-5 DO - 10.1007/s11103-013-0069-5 ID - Tseng2013 ER - TY - JOUR AU - Maier, R. M. AU - Neckermann, K. AU - Igloi, G. L. AU - Kossel, H. PY - 1995 DA - 1995// TI - Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing JO - J Mol Biol VL - 251 UR - https://doi.org/10.1006/jmbi.1995.0460 DO - 10.1006/jmbi.1995.0460 ID - Maier1995 ER - TY - JOUR AU - Sloan, D. B. PY - 2017 DA - 2017// TI - Nuclear and mitochondrial RNA editing systems have opposite effects on protein diversity JO - Biol Lett VL - 13 UR - https://doi.org/10.1098/rsbl.2017.0314 DO - 10.1098/rsbl.2017.0314 ID - Sloan2017 ER - TY - JOUR AU - Kahlau, S. AU - Bock, R. PY - 2008 DA - 2008// TI - Plastid transcriptomics and translatomics of tomato fruit development and chloroplast-to-chromoplast differentiation : chromoplast gene expression largely serves the production of a single protein JO - Plant Cell VL - 20 UR - https://doi.org/10.1105/tpc.107.055202 DO - 10.1105/tpc.107.055202 ID - Kahlau2008 ER - TY - JOUR AU - Valkov, V. T. AU - Scotti, N. AU - Kahlau, S. AU - Maclean, D. AU - Grillo, S. AU - Gray, J. C. PY - 2009 DA - 2009// TI - Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and posttranscriptional control JO - Plant Physiol VL - 150 UR - https://doi.org/10.1104/pp.109.140483 DO - 10.1104/pp.109.140483 ID - Valkov2009 ER - TY - JOUR AU - Swiatek, M. AU - Kuras, R. AU - Sokolenko, A. AU - Higgs, D. AU - Olive, J. AU - Cinque, G. PY - 2001 DA - 2001// TI - The chloroplast gene ycf9 encodes a photosystem II ( PSII ) core subunit, PsbZ, that participates in PSII supramolecular architecture JO - Plant Cell VL - 13 UR - https://doi.org/10.1105/TPC.010001 DO - 10.1105/TPC.010001 ID - Swiatek2001 ER - TY - JOUR AU - Wei, X. AU - Su, X. AU - Cao, P. AU - Liu, X. AU - Chang, W. AU - Li, M. PY - 2016 DA - 2016// TI - Structure of spinach photosystem II – LHCII supercomplex at 3.2 Å resolution JO - Nature VL - 534 UR - https://doi.org/10.1038/nature18020 DO - 10.1038/nature18020 ID - Wei2016 ER - TY - JOUR AU - Kawabe, A. AU - Furihata, H. Y. AU - Tsujino, Y. AU - Kawanabe, T. AU - Fujii, S. AU - Yoshida, T. PY - 2019 DA - 2019// TI - Divergence of RNA editing among Arabidopsis species JO - Plant Sci VL - 280 UR - https://doi.org/10.1016/j.plantsci.2018.12.009 DO - 10.1016/j.plantsci.2018.12.009 ID - Kawabe2019 ER - TY - JOUR AU - Zghidi, W. AU - Merendino, L. AU - Cottet, A. AU - Mache, R. AU - Lerbs-Mache, S. PY - 2007 DA - 2007// TI - Nucleus-encoded plastid sigma factor SIG3 transcribes specifically the psbN gene in plastids JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl1067 DO - 10.1093/nar/gkl1067 ID - Zghidi2007 ER - TY - JOUR AU - Chevalier, F. AU - Ghulam, M. M. AU - Rondet, D. AU - Pfannschmidt, T. AU - Merendino, L. AU - Lerbs-Mache, S. PY - 2015 DA - 2015// TI - Characterization of the psbH precursor RNAs reveals a precise endoribonuclease cleavage site in the psbT/ psbH intergenic region that is dependent on psbN gene expression JO - Plant Mol Biol VL - 88 UR - https://doi.org/10.1007/s11103-015-0325-y DO - 10.1007/s11103-015-0325-y ID - Chevalier2015 ER - TY - JOUR AU - Zghidi-Abouzid, O. AU - Merendino, L. AU - Buhr, F. AU - Ghulam, M. M. AU - Lerbs-Mache, S. PY - 2011 DA - 2011// TI - Characterization of plastid psbT sense and antisense RNAs JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkr143 DO - 10.1093/nar/gkr143 ID - Zghidi-Abouzid2011 ER - TY - JOUR AU - Georg, J. AU - Honsel, A. AU - Rennenberg, H. AU - Hess, W. R. PY - 2010 DA - 2010// TI - Rapid report a long antisense RNA in plant chloroplasts JO - New Phytol VL - 4 UR - https://doi.org/10.1111/j.1469-8137.2010.03203.x DO - 10.1111/j.1469-8137.2010.03203.x ID - Georg2010 ER - TY - JOUR AU - Bollenbach, T. J. AU - Sharwood, R. E. AU - Gutierrez, R. AU - Lerbs-Mache, S. AU - Stern, D. B. PY - 2009 DA - 2009// TI - The RNA-binding proteins CSP41a and CSP41b may regulate transcription and translation of chloroplast-encoded RNAs in Arabidopsis JO - Plant Mol Biol VL - 69 UR - https://doi.org/10.1007/s11103-008-9436-z DO - 10.1007/s11103-008-9436-z ID - Bollenbach2009 ER - TY - JOUR AU - Manavski, N. AU - Schmid, L. M. AU - Meurer, J. PY - 2018 DA - 2018// TI - RNA-stabilization factors in chloroplasts of vascular plants JO - Essays Biochem VL - 62 UR - https://doi.org/10.1042/EBC20170061 DO - 10.1042/EBC20170061 ID - Manavski2018 ER - TY - JOUR AU - Hotto, A. M. AU - Schmitz, R. J. AU - Fei, Z. AU - Ecker, J. R. AU - Stern, D. B. PY - 2011 DA - 2011// TI - Unexpected diversity of chloroplast noncoding RNAs as revealed by deep sequencing of the Arabidopsis transcriptome JO - G3-Genes Genomes Genet VL - 1 UR - https://doi.org/10.1534/g3.111.000752 DO - 10.1534/g3.111.000752 ID - Hotto2011 ER - TY - JOUR AU - Chen, H. AU - Zhang, J. AU - Yuan, G. AU - Liu, C. PY - 2014 DA - 2014// TI - Complex interplay among DNA modification, noncoding RNA expression and protein-coding RNA expression in Salvia miltiorrhiza chloroplast genome JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0099314 DO - 10.1371/journal.pone.0099314 ID - Chen2014 ER - TY - BOOK AU - Marsden-Jones, E. M. AU - Turrill, W. B. PY - 1957 DA - 1957// TI - The bladder campions PB - The Ray Society CY - London ID - Marsden-Jones1957 ER - TY - JOUR AU - Hackl, T. AU - Hedrich, R. AU - Schultz, J. AU - Forster, F. PY - 2014 DA - 2014// TI - Sequence analysis proovread : large-scale high-accuracy PacBio correction through iterative short read consensus JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu392 DO - 10.1093/bioinformatics/btu392 ID - Hackl2014 ER - TY - JOUR AU - Koren, S. AU - Walenz, B. P. AU - Berlin, K. AU - Miller, J. R. AU - Bergman, N. H. AU - Phillippy, A. M. PY - 2017 DA - 2017// TI - Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation JO - Genome Res VL - 27 UR - https://doi.org/10.1101/gr.215087.116 DO - 10.1101/gr.215087.116 ID - Koren2017 ER - TY - STD TI - Beier S, Thiel T, Munich T, Scholz U, Mascher M. Sequence analysis MISA-web: a web server for microsatellite prediction. Bioiformatics. 2017;33:2583–2585. doi: 0.1093/bioinformatics/btx198. ID - ref53 ER - TY - JOUR AU - Robison, T. A. AU - Wolf, P. G. PY - 2019 DA - 2019// TI - ReFernment: an R package for annotating RNA editing in plastid genomes JO - Appl Plant Sci VL - 7 UR - https://doi.org/10.1002/aps3.1216 DO - 10.1002/aps3.1216 ID - Robison2019 ER - TY - JOUR AU - Katoh, K. AU - Standley, D. M. PY - 2013 DA - 2013// TI - MAFFT multiple sequence alignment software version 7: improvements in performance and usability article fast track JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst010 DO - 10.1093/molbev/mst010 ID - Katoh2013 ER - TY - JOUR AU - Simmons, M. P. AU - Ochoterena, H. PY - 2000 DA - 2000// TI - Society of Systematic Biologists gaps as characters in sequence-based phylogenetic analyses JO - Syst Biol VL - 49 UR - https://doi.org/10.1093/sysbio/49.2.369 DO - 10.1093/sysbio/49.2.369 ID - Simmons2000 ER - TY - JOUR AU - Salinas, D. R. AU - Little, D. P. PY - 2014 DA - 2014// TI - 2MATRIX : A utility for indel coding and phylogenetic MATRIX concatenation JO - Appl Plant Sci VL - 2 UR - https://doi.org/10.3732/apps.1300083 DO - 10.3732/apps.1300083 ID - Salinas2014 ER - TY - JOUR AU - Stamatakis, A. PY - 2014 DA - 2014// TI - RAxML version 8 : a tool for phylogenetic analysis and post-analysis of large phylogenies JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu033 DO - 10.1093/bioinformatics/btu033 ID - Stamatakis2014 ER - TY - JOUR AU - Ronquist, F. AU - Teslenko, M. AU - Mark, P. AU - Ayres, D. L. AU - Darling, A. AU - Hohna, S. PY - 2012 DA - 2012// TI - MrBayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space JO - Syst Biol VL - 61 UR - https://doi.org/10.1093/sysbio/sys029 DO - 10.1093/sysbio/sys029 ID - Ronquist2012 ER - TY - STD TI - Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop (GCE), 14 Nov. 2010, New Orleans. LA: IEEE; p 1–8. https://doi.org/10.1109/GCE.2010.5676129. ID - ref60 ER - TY - JOUR AU - Librado, P. AU - Rozas, J. PY - 2009 DA - 2009// TI - DnaSP v5: a software for comprehensive analysis of DNA polymorphism data JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp187 DO - 10.1093/bioinformatics/btp187 ID - Librado2009 ER - TY - JOUR AU - Wu, T. D. AU - Nacu, S. PY - 2010 DA - 2010// TI - Fast and SNP-tolerant detection of complex variants and splicing in short reads JO - Bioinformatics. VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq057 DO - 10.1093/bioinformatics/btq057 ID - Wu2010 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. PY - 2009 DA - 2009// TI - The sequence alignment / map format and SAMtools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - JOUR AU - Thorvaldsdottir, P. PY - 2012 DA - 2012// TI - Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration JO - Brief Bioinform VL - 14 UR - https://doi.org/10.1093/bib/bbs017 DO - 10.1093/bib/bbs017 ID - Thorvaldsdottir2012 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Trapnell, C. AU - Pachter, L. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - TopHat : discovering splice junctions with RNA-Seq JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp120 DO - 10.1093/bioinformatics/btp120 ID - Trapnell2009 ER - TY - JOUR AU - McKenna, A. AU - Hanna, M. AU - Banks, E. AU - Sivachenko, A. AU - Cibulskis, A. AU - Kernytsky, A. PY - 2010 DA - 2010// TI - The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.107524.110 DO - 10.1101/gr.107524.110 ID - McKenna2010 ER - TY - JOUR AU - Wagner, G. P. AU - Kin, K. AU - Lynch, V. J. PY - 2012 DA - 2012// TI - Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples JO - Theory Biosci VL - 131 UR - https://doi.org/10.1007/s12064-012-0162-3 DO - 10.1007/s12064-012-0162-3 ID - Wagner2012 ER -