README

Implementation of the PaPaRa 2.0 algorithm.
Build with 'sh build_papara2.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 (www.boost.org) 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 https://github.com/sim82/papara_nt