README

PNPProbs (2014)

PNPProbs is an open source program to align multiple sequences 
combining progressive and non-progressive alignment approaches.
The program is developed by Yongtao Ye (ytye@cs.hku.hk)  
using open source codes of GLProbs (written by Y. Ye) 
and PicXAA (written by S. Mohammad Ebrahim Sahraeian and Byung-Jun Yoon).
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Install:

You will need a Unix environment with a working C++ compiler to
compile the PNPProbs source. 

Type
$ make
$ make install

If you want to clean the compiled results, you may type "make clean".

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Usage:
       pnpprobs [OPTION]... [infile]...

Description:
       Align sequences in multi-FASTA format

       -o, --outfile <string>
              specify the output file name (STDOUT by default)

       -num_threads <integer>
              specify the number of threads used, and otherwise detect automatically

       -clustalw
              use CLUSTALW output format instead of FASTA format

       -c, --consistency REPS
              use 0 <= REPS <= 5 (default: 2) passes of consistency transformation

       -ir, --iterative-refinement REPS
              use 0 <= REPS <= 1000 (default: 100) passes of iterative-refinement

       -v, --verbose
              report progress while aligning (default: off)

       -timeon, -timeoff
              report program running times of each step (default:on)

       -annot FILENAME
              write annotation for multiple alignment to FILENAME

       -a, --alignment-order
              print sequences in alignment order rather than input order (default: off)

       -version 
              print out version of GLProbs 

Typical used example:
./pnpprobs infile >outfile or ./pnpprobs infile -o outfile
N.B. The alignments are printed out into file "outfile" in FASTA format