Graham PH, Vance CP. Legumes: importance and constraints to greater use. Plant Physiol. 2003;131:872–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kami J, Velásquez VB, Debouck DG, Gepts P. Identification of presumed ancestral DNA sequences of phaseolin in Phaseolus vulgaris. Proc Natl Acad Sci U S A. 1995;92:1101–4.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kwak M, Gepts P. Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae). Theor Appl Genet. 2009;118:979–92.
Article
CAS
PubMed
Google Scholar
Bitocchi E, Nanni L, Bellucci E, Rossi M, Giardini A, Zeuli PS, et al. Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data. Proc Natl Acad Sci U S A. 2012;109:E788–96.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mamidi S, Rossi M, Moghaddam SM, Annam D, Lee R, Papa R, et al. Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L. Heredity (Edinb). 2013;110:267–76.
Article
CAS
Google Scholar
Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet. 2014;46:707–13.
Article
CAS
PubMed
Google Scholar
Mamidi S, Rossi M, Annam D, Moghaddam S, Lee R, Papa R, et al. Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data. Funct Plant Biol. 2011;38:953–67.
Article
CAS
Google Scholar
Gepts P. Origin and evolution of common bean: Past events and recent trends. HortScience. 1998;33:1124–30.
Google Scholar
Chacón SMI, Pickersgill B, Debouck DG. Domestication patterns in common bean (Phaseolus vulgaris L.) and the origin of the Mesoamerican and Andean cultivated races. Theor Appl Genet. 2005;110:432–44.
Article
Google Scholar
Delgado-Salinas A, Bibler R, Lavin M. Phylogeny of the genus Phaseolus (Leguminosae): a recent diversification in an ancient landscape. Syst Bot. 2006;31:779–91.
Article
Google Scholar
Bitocchi E, Bellucci E, Giardini A, Rau D, Rodriguez M, Biagetti E, et al. Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes. New Phytol. 2013;197(1):300–13.
Article
CAS
PubMed
Google Scholar
Papa R, Gepts P. Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica. Theor Appl Genet. 2003;106:239–50.
CAS
PubMed
Google Scholar
Papa R, Acosta-Gallegos JA, Delgado-Salinas A, Gepts P. A genome-wide analysis of differentiation between wild and domesticated Phaseolus vulgaris from Mesoamerica. Theor Appl Genet. 2005;111:1147–58.
Article
CAS
PubMed
Google Scholar
Blair MW, Soler A, Cortés AJ. Diversification and population structure in common beans (Phaseolus vulgaris L.). PLoS One. 2012;7:e49488.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gaut BS. The complex domestication history of the common bean. Nat Genet. 2014;46:663.
Article
CAS
PubMed
Google Scholar
Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, et al. High-throughput genotyping by whole-genome resequencing. Genome Res. 2009;19:1068–76.
Article
PubMed Central
CAS
PubMed
Google Scholar
Arumuganathan K, Earle E. Nuclear DNA content of some important plant species. Plant Mol Biol Report. 1991;9:208–18.
Article
CAS
Google Scholar
Bennett MD, Smith JB. Nuclear DNA amounts in angiosperms. Philos Trans R Soc Lond B Biol Sci. 1976;274:227–74.
Article
CAS
PubMed
Google Scholar
Parra G, Bradnam K, Korf I. CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007;23:1061–7.
Article
CAS
PubMed
Google Scholar
Arimura G, Ozawa R, Kugimiya S, Takabayashi J, Bohlmann J. Herbivore-induced defense response in a model legume. Two-spotted spider mites induce emission of (E)-beta-ocimene and transcript accumulation of (E)-beta-ocimene synthase in Lotus japonicus. Plant Physiol. 2004;135(4):1976–83.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kelly JD, Gepts P, Miklas PN, Coyne DP. Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic importance in bean and cowpea. Field Crops Res. 2003;82:135–54.
Article
Google Scholar
Geffroy V, Sévignac M, De Oliveira JC, Fouilloux G, Skroch P, Thoquet P, et al. Inheritance of partial resistance against Colletotrichum lindemuthianum in Phaseolus vulgaris and co-localization of quantitative trait loci with genes involved in specific resistance. Mol Plant Microbe Interact. 2000;13:287–96.
Article
CAS
PubMed
Google Scholar
Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, et al. Long noncoding RNAs with enhancer-like function in human cells. Cell. 2010;143:46–58.
Article
PubMed Central
PubMed
Google Scholar
Huerta-Cepas J, Capella-Gutiérrez S, Pryszcz LP, Marcet-Houben M, Gabaldón T. PhylomeDB v4: Zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res. 2014;42:D897–902.
Article
PubMed Central
CAS
PubMed
Google Scholar
Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, Marcet-Houben M, et al. PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res. 2011;39:D556–60.
Article
PubMed Central
CAS
PubMed
Google Scholar
Huerta-Cepas J, Gabaldón T. Assigning duplication events to relative temporal scales in genome-wide studies. Bioinformatics. 2011;27:38–45.
Article
CAS
PubMed
Google Scholar
Gabaldón T. Large-scale assignment of orthology: back to phylogenetics? Genome Biol. 2008;9:235.
Article
PubMed Central
PubMed
Google Scholar
Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, et al. Ancestral polyploidy in seed plants and angiosperms. Nature. 2011;473:97–100.
Article
CAS
PubMed
Google Scholar
Yang Y, Moore MJ, Brockington SF, Soltis DE, Wong GK. Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Mol Biol Evol 2015;32(8):2001–14.
Article
PubMed
Google Scholar
Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, et al. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A. 2006;103:14959–64.
Article
PubMed Central
CAS
PubMed
Google Scholar
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463:178–83.
Article
CAS
PubMed
Google Scholar
Fernández F, Paul G, Marceliano L. Stages of development of the common bean plant ed. Cali, Colombia: Centro Internacional De Agricultura Tropical (CIAT); 1986.
García Mendoza Efraín A. Guía técnica para el cultivo del fríjol. Iica-Red. 2009. http://repiica.iica.int/DOCS/B2170E/B2170E.PDF. Accessed 5 Feb 2016.
Bellucci E, Bitocchi E, Ferrarini A, Benazzo A, Biagetti E, Klie S, et al. Decreased nucleotide and expression diversity and modified coexpression patterns characterize domestication in the common bean. Plant Cell. 2014;26:1901–12.
Article
PubMed Central
CAS
PubMed
Google Scholar
O’Rourke J, Iniguez LP, Fu F, Bucciarelli B, Miller SS, Jackson S, et al. An RNA-Seq based gene expression atlas of the common bean. BMC Genomics. 2014;15:866.
Article
PubMed Central
PubMed
Google Scholar
Severin AJ, Woody JL, Bolon Y-T, Joseph B, Diers BW, Farmer AD, et al. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol. 2010;10:160.
Article
PubMed Central
PubMed
Google Scholar
Mao L, Van Hemert JL, Dash S, Dickerson JA. Arabidopsis gene co-expression network and its functional modules. BMC Bioinformatics. 2009;10:346.
Article
PubMed Central
PubMed
Google Scholar
Ohno S. Evolution by gene duplication. ed. Berlin, Heidelberg: Springer Berlin Heidelberg; 1970. doi:10.1007/978-3-642-86659-3.
Huerta-cepas J, Dopazo J, Huynen M, Gabaldón T. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Brief Bioinform. 2011;12:442–8.
Article
CAS
PubMed
Google Scholar
Padawer T, Leighty RE, Wang D. Duplicate gene enrichment and expression pattern diversification in multicellularity. Nucleic Acids Res. 2012;40:7597–605.
Article
PubMed Central
CAS
PubMed
Google Scholar
McConnell M, Mamidi S, Lee R, Chikara S, Rossi M, Papa R, et al. Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.). Theor Appl Genet. 2010;121:1103–16.
Article
PubMed
Google Scholar
Ramírez M, Graham M, Blanco-lo L, Silvente S, Medrano-soto A, Blair MW, et al. Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol. 2005;137(April):1211–27.
Article
PubMed Central
PubMed
Google Scholar
Melotto M, Monteiro-Vitorello CB, Bruschi AG, Camargo LEA, Belzile F. Comparative bioinformatic analysis of genes expressed in common bean (Phaseolus vulgaris L.) seedlings. Genome. 2005;48:562–70.
Article
CAS
PubMed
Google Scholar
Tian J, Venkatachalam P, Liao H, Yan X, Raghothama K. Molecular cloning and characterization of phosphorus starvation responsive genes in common bean (Phaseolus vulgaris L.). Planta. 2007;227:151–65.
Article
CAS
PubMed
Google Scholar
Kalavacharla V, Liu Z, Meyers BC, Thimmapuram J, Melmaiee K. Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing. BMC Plant Biol. 2011;11:135.
Article
PubMed Central
CAS
PubMed
Google Scholar
Le BH, Wagmaister J, Kawashima T, Bui AQ, Harada JJ, Goldberg RB. Using genomics to study legume seed development. Plant Physiol. 2007;144(June):562–74.
Article
PubMed Central
CAS
PubMed
Google Scholar
Singh VK, Garg R, Jain M. A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant Biotechnol J. 2013;11:691–701.
Article
CAS
PubMed
Google Scholar
Verdier J, Torres-Jerez I, Wang M, Andriankaja A, Allen SN, He J, et al. Establishment of the Lotus japonicus Gene Expression Atlas (LjGEA) and its use to explore legume seed maturation. Plant J. 2013;74:351–62.
Article
CAS
PubMed
Google Scholar
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res. 2012;22:1775–89.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sun J, Lin Y, Wu J. Long non-coding RNA expression profiling of mouse testis during postnatal development. PLoS One. 2013;8:e75750.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kutter C, Watt S, Stefflova K, Wilson MD, Goncalves A, Ponting CP, et al. Rapid turnover of long noncoding RNAs and the evolution of gene expression. PLoS Genet. 2012;8:e1002841.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mutwil M, Usadel B, Schütte M, Loraine A, Ebenhöh O, Persson S. Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm. Plant Physiol. 2010;152:29–43.
Article
PubMed Central
CAS
PubMed
Google Scholar
Aoki K, Ogata Y, Shibata D. Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol. 2007;48:381–90.
Article
CAS
PubMed
Google Scholar
Ma S, Shah S, Bohnert HJ, Snyder M, Dinesh-Kumar SP. Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways. PLoS Genet. 2013;9:e1003840.
Article
PubMed Central
PubMed
Google Scholar
Lynch M, Force A. The probability of duplicate gene preservation by subfunctionalization. Genetics. 2000;154:459–73.
PubMed Central
CAS
PubMed
Google Scholar
Prince VE, Pickett FB. Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet. 2002;3:827–37.
Article
CAS
PubMed
Google Scholar
Renny-Byfield S, Gallagher JP, Grover CE, Szadkowski E, Page JT, Udall JA, et al. Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biol Evol. 2014;6:559–71.
Article
PubMed Central
CAS
PubMed
Google Scholar
Duarte JM, Cui L, Wall PK, Zhang Q, Zhang X, Leebens-Mack J, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol Biol Evol. 2006;23:469–78.
Article
CAS
PubMed
Google Scholar
Ferreira RMB, Ramos PCR, Franco E, Ricardo CPP, Teixeira ARN. Changes in ubiquitin and ubiquitin-protein conjugates during seed formation and germination. J Exp Bot. 1995;46:211–9.
Article
CAS
Google Scholar
Geffroy V, Sicard D, de Oliveira JC, Sévignac M, Cohen S, Gepts P, et al. Identification of an ancestral resistance gene cluster involved in the coevolution process between Phaseolus vulgaris and its fungal pathogen Colletotrichum lindemuthianum. Mol Plant Microbe Interact. 1999;12:774–84.
Article
CAS
PubMed
Google Scholar
Chisholm ST, Coaker G, Day B, Staskawicz BJ. Host-microbe interactions: shaping the evolution of the plant immune response. Cell. 2006;124(4):803–14.
Article
CAS
PubMed
Google Scholar
Cook DE, Lee TG, Guo X, Melito S, Wang K, Bayless AM, et al. Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science. 2012;338:1206–9.
Article
CAS
PubMed
Google Scholar
Delgado-Salinas A, López S. Diversidad y distribución de los frijoles silvestres en México. Revista Digital Universitaria. 2015. http://www.revista.unam.mx/vol.16/num2/art10/. Accessed 5 Feb 2016
Grisi MCM, Blair MW, Gepts P, Brondani C, Pereira PAA, Brondani RPV. Genetic mapping of a new set of microsatellite markers in a reference common bean (Phaseolus vulgaris) population BAT93 x Jalo EEP558. Genet Mol Res. 2007;6:691–706.
CAS
PubMed
Google Scholar
Newbler assembler. Available at: http://454.com/products/analysis-software/index.asp. Accessed 5 Feb 2016.
Flutre T, Duprat E, Feuillet C, Quesneville H. Considering transposable element diversification in de novo annotation approaches. PLoS One. 2011;6:e16526.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ellinghaus D, Kurtz S, Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics. 2008;9:18.
Article
PubMed Central
PubMed
Google Scholar
Steinbiss S, Willhoeft U, Gremme G, Kurtz S. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Res. 2009;37:7002–13.
Article
PubMed Central
CAS
PubMed
Google Scholar
Smit A, Hubley R, Green P. RepeatMasker Open-3.0. 1996. Available at: http://www.repeatmasker.org/. Accessed 5 Feb 2016.
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110:462–7.
Article
CAS
PubMed
Google Scholar
Benson D, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013;41:D36-42.
EMBL SIB. Swiss Institute of Bioinformatics, Protein Information Resource (PIR). UniProt. Nucleic Acids Res. 2013;41:D43–7.
Article
Google Scholar
Blanco E, Parra G, Guigó R. Using geneid to identify genes. Curr Protoc Bioinformatics. 2007; Chapter 4:Unit 4.3. doi:10.1002/0471250953.bi0403s18.
Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, Guigo R. Comparative gene prediction in human and mouse. Genome Res. 2003;13:108–17.
Article
PubMed Central
CAS
PubMed
Google Scholar
Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. AUGUSTUS: Ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006;34:W435–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Majoros WH, Pertea M, Salzberg SL. TigrScan and GlimmerHMM: Two open source ab initio eukaryotic gene-finders. Bioinformatics. 2004;20:2878–9.
Article
CAS
PubMed
Google Scholar
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 2008;9:R7.
Article
PubMed Central
PubMed
Google Scholar
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, et al. InterPro in 2011: New developments in the family and domain prediction database. Nucleic Acids Res. 2012;40:D306–12.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012;40:D109–14.
Article
PubMed Central
CAS
PubMed
Google Scholar
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, et al. The Reactome pathway knowledgebase. Nucleic Acids Res. 2014;42:D472–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8:785–6.
Article
CAS
PubMed
Google Scholar
Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008;36:3420–35.
Article
PubMed Central
PubMed
Google Scholar
Sanseverino W, Hermoso A, D’Alessandro R, Vlasova A, Andolfo G, Frusciante L, et al. PRGdb 2.0: Towards a community-based database model for the analysis of R-genes in plants. Nucleic Acids Res. 2013;41:D1167–71.
Article
PubMed Central
CAS
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Article
CAS
PubMed
Google Scholar
Slater GSC, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005;6:31.
Article
PubMed Central
PubMed
Google Scholar
Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000;302:205–17.
Article
CAS
PubMed
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nat Biotechnol. 2011;28:511–5.
Article
Google Scholar
Sammeth M. Flux Capacitor. Available at: http://sammeth.net/confluence/display/FLUX/Home. Accessed 5 Feb 2016.
Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: Inference of RNA alignments. Bioinformatics. 2009;25:1335–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Griebel T, Marco-Sola S. GEM-Tools. Available at: https://github.com/gemtools/gemtools. Accessed 5 Feb 2016.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5:621–8.
Article
CAS
PubMed
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Article
PubMed Central
CAS
PubMed
Google Scholar
Alexa A, Rahnenführer J. topGO: topGO: Enrichment analysis for Gene Ontology. R package, 2010, Available at: http://www.bioconductor.org/packages/release/bioc/html/topGO.html. Accessed 5 Feb 2016.
Friedman J, Hastie T, Tibshirani R. Sparse inverse covariance estimation with the graphical lasso. Biostatistics. 2008;9:432–41.
Article
PubMed Central
PubMed
Google Scholar
Fruchterman T, Reingold M. Graph drawing by force-directed placement. Software Practice Experience. 1991;21:1129–64.
Article
Google Scholar
Clauset A, Newman ME, Moore C. Finding community structure in very large networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2004;70(6 Pt 2):066111.
Article
PubMed
Google Scholar
Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5:113.
Article
PubMed Central
PubMed
Google Scholar
Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008;9:286–98.
Article
CAS
PubMed
Google Scholar
Lassmann T, Frings O, Sonnhammer ELL. Kalign2: High-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acids Res. 2009;37:858–65.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wallace IM, O’Sullivan O, Higgins DG, Notredame C. M-Coffee: Combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006;34:1692–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.
Article
PubMed Central
PubMed
Google Scholar
Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol. 1997;14:685–95.
Article
CAS
PubMed
Google Scholar
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21.
Article
CAS
PubMed
Google Scholar
Huerta-Cepas J, Dopazo J, Gabaldón T. ETE: a python environment for tree exploration. BMC Bioinformatics. 2010;11:24.
Article
PubMed Central
PubMed
Google Scholar
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012;40(D1):D1178–86.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–95.
Article
PubMed Central
PubMed
Google Scholar