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1 parent f9d3905 commit 9d2224087ca83cf3b6ca6265936d6298c9c71b89 @sim82 committed Feb 7, 2012
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  1. +16 −0 README
  2. +7 −0 build_papara2.sh
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16 README
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+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
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7 build_papara2.sh
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+#!/bin/sh
+
+# minimal build script for papara 2.0.
+# please use the supplied cmake files for anything more than just building papara 2.0.
+
+g++ -o papara -O3 papara.cpp -I ivy_mike/src/ -I ublasJama-1.0.2.3 sequence_model.cpp parsimony.cpp ivy_mike/src/time.cpp ivy_mike/src/tree_parser.cpp ivy_mike/src/getopt.cpp ivy_mike/src/demangle.cpp ivy_mike/src/multiple_alignment.cpp ublasJama-1.0.2.3/EigenvalueDecomposition.cpp -lpthread
+

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