GitHub - sim82/papara_nt: new codebase of the PaPaRa algorithm

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Name		Name	Last commit message	Last commit date
Latest commit History 243 Commits
ivy_mike @ 3269b7b		ivy_mike @ 3269b7b
old		old
ublasJama-1.0.2.3		ublasJama-1.0.2.3
.gitignore		.gitignore
.gitmodules		.gitmodules
CMakeLists.txt		CMakeLists.txt
LICENSE		LICENSE
README		README
align_pvec_vec.h		align_pvec_vec.h
align_utils.cpp		align_utils.cpp
align_utils.h		align_utils.h
align_vec.h		align_vec.h
blast_partassign.cpp		blast_partassign.cpp
blast_partassign.h		blast_partassign.h
build_extern.sh		build_extern.sh
build_papara2.sh		build_papara2.sh
build_papara2_static.sh		build_papara2_static.sh
call_main2.cpp		call_main2.cpp
dtw.cpp		dtw.cpp
dtw.h		dtw.h
dump_anc_probs.cpp		dump_anc_probs.cpp
epa_extract_qs_covered.cpp		epa_extract_qs_covered.cpp
fasta_random_sample.cpp		fasta_random_sample.cpp
fasta_random_sample2.cpp		fasta_random_sample2.cpp
fasta_to_phy.cpp		fasta_to_phy.cpp
inherit_test.cpp		inherit_test.cpp
main.cpp		main.cpp
math_approx.h		math_approx.h
nacl_32.cmake		nacl_32.cmake
pairwise_seq_distance.cpp		pairwise_seq_distance.cpp
pairwise_seq_distance.h		pairwise_seq_distance.h
papara.cpp		papara.cpp
papara.h		papara.h
papara2_main.cpp		papara2_main.cpp
pars_align_gapp_seq.cpp		pars_align_gapp_seq.cpp
pars_align_gapp_seq.h		pars_align_gapp_seq.h
pars_align_seq.cpp		pars_align_seq.cpp
pars_align_seq.h		pars_align_seq.h
parsimony.cpp		parsimony.cpp
parsimony.h		parsimony.h
phy_cut_partition.cpp		phy_cut_partition.cpp
phy_megamerge.cpp		phy_megamerge.cpp
phy_to_fasta.cpp		phy_to_fasta.cpp
prepare_extern.sh		prepare_extern.sh
propara.cpp		propara.cpp
pvec.cpp		pvec.cpp
pvec.h		pvec.h
pw_dist.cpp		pw_dist.cpp
raw_to_phy.rb		raw_to_phy.rb
raxml_interface.cpp		raxml_interface.cpp
raxml_interface.h		raxml_interface.h
ro_submodules.sh		ro_submodules.sh
sequence_model.cpp		sequence_model.cpp
sequence_model.h		sequence_model.h
small.tree		small.tree
smith_waterman.cpp		smith_waterman.cpp
stepwise_addition.cpp		stepwise_addition.cpp
stepwise_addition_gapp.cpp		stepwise_addition_gapp.cpp
stepwise_addition_pro.cpp		stepwise_addition_pro.cpp
stepwise_align.h		stepwise_align.h
tar_release.sh		tar_release.sh
tbb.cpp		tbb.cpp
test_bitset.cpp		test_bitset.cpp
testbench.cpp		testbench.cpp
tree_similarity.cpp		tree_similarity.cpp
tree_similarity.h		tree_similarity.h
tree_utils.h		tree_utils.h
vec_unit.h		vec_unit.h

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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