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Estimation of recombination

EC Emeline Cherchame
LG Laurent Guillier
RL Renaud Lailler
MV Marie-Leone Vignaud
NS Nathalie Jourdan-Da Silva
SH Simon Le Hello
FW François-Xavier Weill
SC Sabrina Cadel-Six
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Recombination events were detected and the branch lengths were corrected taking into account the phylogenetic reconstruction obtained with the ClonalFrameML tool, as described by Diderot et al. in 2015 [55]. We used as input files the ML tree generated using the IQ-TREE tool and the pseudogenome file obtained using the iVARCall2 workflow. The R/theta rate, ratio of frequency of recombination and mutation, was directly obtained in the ClonalFrameML output. The r/m rate, ratio of effects of recombination and mutation, was calculated using the formula r/m = R/theta*delta*nu.

In order to produce a SNP distance matrix excluding variants linked to recombination events (> 400 bp), the script ‘Clonal_VCFilter’ [51] was applied.

The phylogenetic inference was corrected, accounting for the detected recombinations. Trees were visualized and annotated using R package ggtree [56, 57].

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