Data from: Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)

Sveinsson S, Cronk Q

Date Published: December 4, 2014

DOI: http://dx.doi.org/10.5061/dryad.km38g

 

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Title Trifolium_plastid_coding
Downloaded 5 times
Description A concatenated matrix of 59 protein coding plastid genes. Only coding regions were used, introns and intergenic regions were excluded in the alignment, due to plastome rearrangements (see manuscript of further description). The alignment was generated using Mafft v7.053b using -auto flag and trimmed using TrimAl with the -automated1 flag. This process was pipelined using Plast2Phy (https://github.com/saemi/plast2phy).
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Title Trifolium_plastid_coding_ML
Downloaded 7 times
Description ML tree generated using GARLI (the config file is the ReadMe file). The model used GTR+G, based on a jModelTest search and an AIC test. 10 starts were prefromed and a 100 bootstrap replicates. Medicago truncatula is the outrgroup.
Download Trifolium_plastid_coding_ML.tre (7.596 Kb)
Download README.conf (1.291 Kb)
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When using this data, please cite the original publication:

Sveinsson S, Cronk Q (2014) Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium). BMC Evolutionary Biology 14:228. http://dx.doi.org/10.1186/s12862-014-0228-6

Additionally, please cite the Dryad data package:

Sveinsson S, Cronk Q (2014) Data from: Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.km38g
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