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new codebase of the PaPaRa algorithm
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ivy_mike @ 8a000ce added phy_megamerge: merge sequences from multiple (multi-gene) phyli…
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ublasJama-1.0.2.3
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CMakeLists.txt
LICENSE
README
align_pvec_vec.h
align_utils.cpp forgot file
align_utils.h
align_vec.h Merge branch 'cpp11' into common_cpp
blast_partassign.cpp added phy_cut_partition for cutting sindividual partitions out of lar…
blast_partassign.h
build_extern.sh
build_papara2.sh
call_main2.cpp
dtw.cpp
dtw.h
dump_anc_probs.cpp got propara back into working shape.
epa_extract_qs_covered.cpp
fasta_random_sample.cpp switched to gpl 3.
fasta_random_sample2.cpp
fasta_to_phy.cpp
inherit_test.cpp
main.cpp
math_approx.h more c++11 windows fixes
nacl_32.cmake
pairwise_seq_distance.cpp Merge branch 'cpp11' into common_cpp
pairwise_seq_distance.h
papara.cpp support '.' character (gap)
papara.h fixed crash in the alignment kernel, which was (hopefully) casued by …
papara2_main.cpp
pars_align_gapp_seq.cpp switched to gpl 3.
pars_align_gapp_seq.h Merge branch 'cpp11' into common_cpp
pars_align_seq.cpp
pars_align_seq.h
parsimony.cpp switched to gpl 3.
parsimony.h switched to gpl 3.
phy_cut_partition.cpp
phy_megamerge.cpp
phy_to_fasta.cpp
prepare_extern.sh
propara.cpp
pvec.cpp switched to gpl 3.
pvec.h
pw_dist.cpp switched to gpl 3.
raw_to_phy.rb
raxml_interface.cpp
raxml_interface.h
ro_submodules.sh
sequence_model.cpp Merge branch 'cpp11' into common_cpp
sequence_model.h support '.' character (gap)
small.tree some initial stuff
smith_waterman.cpp switched to gpl 3.
stepwise_addition.cpp Merge branch 'cpp11' into common_cpp
stepwise_addition_gapp.cpp
stepwise_addition_pro.cpp more c++11 windows fixes
stepwise_align.h
tar_release.sh update tar_release.sh
tbb.cpp
test_bitset.cpp
testbench.cpp Merge branch 'cpp11' into common_cpp
tree_similarity.cpp
tree_similarity.h
tree_utils.h
vec_unit.h

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
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