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. 2014 Mar 11;5:70. doi: 10.3389/fpls.2014.00070

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Copyright © 2014 Nguyen, Ranwez, Vile, Soulié, Dellagi, Expert and Gosti.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Phylogeny of the 1 kb-upstream region of the studied PDF1s using an alignment free method. Phylogeny analysis of the 1 kb-long upstream sequence for the 17 studied PDF1 genes: 10 from A. halleri and 7 from A. thaliana (green boxes). Phylogeny inference was carried out using FFP software (Sims et al., 2009), which involves an alignment-free approach based on k-mer frequencies. The bootstrap value obtained with 100 replicates is indicated for each clade. Strongly supported clades (bootstrap support ≥ 95%) are indicated by a red rectangle. These supported clades were consistently recovered when the analysis was conducted with 500 bp upstream restriction sequences.