Skip to content


Subversion checkout URL

You can clone with
Download ZIP
Branch: master
Fetching contributors…

Cannot retrieve contributors at this time

40 lines (35 sloc) 2.1 KB
\section{Finding Recombination Breakpoints}
Bootscanning is a technique for finding recombination breakpoints in a
sequence. The original procedure \cite{Salminen_1995} uses the bootstrap value
of competing topologies as a criterion, the procedure shown below uses the
patristic distance (\ie, distance along the tree) according to the most likely
tree, and is thus not strictly speaking a bootscan but a distance
plot.\footnote{Thanks to Heiko Schmidt for pointing this out.} It involves
aligning the sequence of interest (called \emph{query} or \emph{reference})
with related sequences (including the putative recombinant's parents) and
computing phylogenies locally over the alignment. Recombination is expected to
cause changes in topology. The tasks involved are shown below:
\item align the sequences $\rightarrow$ multiple alignment
\item slice the multiple alignment $\rightarrow$ slices
\item build a tree for each slice $\rightarrow$ trees
\item extract distance from query to other sequences (each tree) $\rightarrow$ tabular data
\item plot data $\rightarrow$ graphics
The distribution contains a script, \texttt{src/}, that performs the whole process. Here is an example run:
$ HRV_3UTR.dna HRV-93 CL073908
where \texttt{HRV\_3UTR.dna} is a FastA file of (unaligned) sequences, \texttt{HRV-93} is the outgroup, and \texttt{CL073908} is the query. Here is the result:
\noindent{}until position 450 or so, the query sequence's nearest relatives (in
terms of substitutions/site) are \texttt{HRV-36} and \texttt{HRV-89}. After
that point, it is \texttt{HRV-67}. This suggests that there is a recombination
breakpoint near position 450.
The script uses \reroot{} to reroot the trees on the outgroup, \clade{} and
\labels{} to get the labels of the ingroup, \distance{} to extract the distance
between the query and the other sequences, as well as the usual \texttt{sed}, \texttt{grep}, etc. The plot is done with gnuplot.
Jump to Line
Something went wrong with that request. Please try again.