GitHub - danfdeblasio/PMFastR: This is a slightly modified version of PMFastR developed while at UCF. See genome.ucf.edu/PMFastR for more info.

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This is a slightly modified version of PMFastR developed while at UCF. See genome.ucf.edu/PMFastR for more info.

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Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
examples		examples
Makefile		Makefile
README		README
examples.sh		examples.sh
fastalignment.5.cc		fastalignment.5.cc
fastalignment.5.h		fastalignment.5.h
fastalignment.6.cc		fastalignment.6.cc
fastalignment.6.h		fastalignment.6.h
fastalignment.8.cc		fastalignment.8.cc
fastalignment.8.h		fastalignment.8.h
fatest1.cc		fatest1.cc
fatest5.cc		fatest5.cc
fatest6.cc		fatest6.cc
filebuffer.cc		filebuffer.cc
filebuffer.h		filebuffer.h
na.h		na.h
queue.cc		queue.cc
queue.h		queue.h
simple_queue.cc		simple_queue.cc
simple_queue.h		simple_queue.h
stack.cc		stack.cc
stack.h		stack.h
stk_profile.cc		stk_profile.cc
stk_profile.h		stk_profile.h
stockholmbuffer.cc		stockholmbuffer.cc
stockholmbuffer.h		stockholmbuffer.h
weight3.h		weight3.h

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This package includes a make file.  This should be used to create all of the necessary files to run the program.  to compile simply run:

>make

The outputs are:

rna_compare5 - This takes in a single sequence (stk format) and a query (fasta format) and an output filename (stok format)

rna_compare6 - This is a single thread version of the alignment takes in a profile (stok format) and a query (fasta format) and an output file name (stok format)

rna_compare8 - this is a multi threaded version of rna_compare6, same input parameters