Additional file 9.
Figure S7. Phylogenetic tree of VIPER elements. Description: Maximum likelihood phylogenetic tree of VIPER retroelements from T. c. marinkellei, T. c. cruzi CLBR, T. c. cruzi X10. The colors correspond to; blue (Tcm), green (Tcc CLBR), red (Tcc X10). VIPER elements were identified with RepeatMasker and only elements longer than 2000 bp were included: 209 sequences in total (35 from Tcm, 57 from Tcc X10 and 117 from Tcc CLBR). The average branch lengths were; 0.0682 (Tcm), 0.039 (Tcc X10), 0.0455 (Tcc CLBR). The alignment was constructed with ClustalW and manually inspected. Gblocks was used to remove ambiguities from the alignment, which resulted in a total of 1518 positions that were used for inferring the phylogeny. The maximum likelihood tree was inferred with RAxML using the GTRCAT model and 100 bootstrap replicates.
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Franzén et al. BMC Genomics 2012 13:531 doi:10.1186/1471-2164-13-531