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Operating Systems OS X (Apple) An Audio Function Generator... Post 302970036 by wisecracker on Thursday 31st of March 2016 03:39:11 PM
Old 03-31-2016
Hi Scrutinizer...

Thanks that is what I needed...

I hadn't researched that yet as it was unimportant at this point in time... :-)
 

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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)
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