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Implementation of the PaPaRa 2.0 algorithm.
Build with 'sh' which will produce the executable 'papara'.
Alternatively you can use the supplied cmake files. To be able to compile the sources you need a resonably recent version
of the boost ( libraries.
Invoke PaPaRa using "./papara -t <ref tree> -s <phylip RA> -q <fasta QS>".
The phylip file (option -s) must contain the reference alignment, consistent with the reference tree (option -t).
The FASTA file (option -q) contains the unaligned QS. Optionally, all sequences which are in <phylip RA> but do not occur in the <ref tree> are also interpreted as QS.
The alignment parameters can be modified using the (optional) option -p <user_options>. <user options> is a string and must have the following form:
"<gap_open>:<gap_extend>:<mismatch>:<match_cgap>", so the default parameters used given in the paper correspond to the user option "-p -3:-1:2:-3".
The output alignment will be written to papara_alignment.default (you can change the file suffix (i.e., "default") by supplying a run-name with parameter '-n'.
You can invoke the multi threaded version by adding the option '-j <num threads>'.
The latest source code is available at