VERSION:(1)							   User Commands						       VERSION:(1)

NAME

       PyNAST - alignment of short DNA sequences

SYNOPSIS

       pynast [options] {-i input_fp -t template_fp}

DESCRIPTION

       [] indicates optional input (order unimportant) {} indicates required input (order unimportant)

   Example usage:
	      pynast -i my_input.fasta -t my_template.fasta

OPTIONS

       --version
	      show program's version number and exit

       -h, --help
	      show this help message and exit

       -t TEMPLATE_FP, --template_fp=TEMPLATE_FP
	      path to template alignment file [REQUIRED]

       -i INPUT_FP, --input_fp=INPUT_FP
	      path to input fasta file [REQUIRED]

       -v, --verbose
	      Print status and other information during execution [default: False]

       -p MIN_PCT_ID, --min_pct_id=MIN_PCT_ID
	      minimum percent sequence	identity to consider a sequence a match [default: 75.0]

       -l MIN_LEN, --min_len=MIN_LEN
	      minimum sequence length to include in NAST alignment [default: 1000]

       -m PAIRWISE_ALIGNMENT_METHOD, --pairwise_alignment_method=PAIRWISE_ALIGNMENT_METHOD
	      method for performing pairwise alignment [default: uclust]

       -a FASTA_OUT_FP, --fasta_out_fp=FASTA_OUT_FP
	      path to store resulting alignment file [default: derived from input filepath]

       -g LOG_FP, --log_fp=LOG_FP
	      path to store log file [default: derived from input filepath]

       -f FAILURE_FP, --failure_fp=FAILURE_FP
	      path to store file of seqs which fail to align [default: derived from input filepath]

       -e MAX_E_VALUE, --max_e_value=MAX_E_VALUE
	      Depreciated. Will be removed in PyNAST 1.2

       -d BLAST_DB, --blast_db=BLAST_DB
	      Depreciated. Will be removed in PyNAST 1.2

SEE ALSO

       http://pynast.sourceforge.net

Version: pynast 1.1						    August 2011 						       VERSION:(1)