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pynast

alignment of short DNA sequences

The package provices a reimplementation of the Nearest Alignment Space Termination tool in Python. It was prepared for next generation sequencers.

Given a set of sequences and a template alignment, PyNAST will align the input sequences against the template alignment, and return a multiple sequence alignment which contains the same number of positions (or columns) as the template alignment. This facilitates the analysis of new sequences in the context of existing alignments, and additional data derived from existing alignments such as phylogenetic trees. Because any protein or nucleic acid sequences and template alignments can be provided, PyNAST is not limited to the analysis of 16s rDNA sequences.

Homepage:
Package version:1.1-3
Architecture:all
Distribution:Debian
Filename:pynast_1.1-3_all.deb

/usr/share/doc/pynast/README

PyNAST documentation
==================================

The PyNAST documentation is available at http://pynast.sourceforge.net. These documents will refer to the latest release version of PyNAST. If you're working with an svn version of PyNAST, you should refer to the documentation in PyNAST/doc/.

Stay up-to-date on PyNAST news
==============================
Subscribing to the PyNAST blog (http:
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/usr/share/doc/pynast/README.Debian

PyNAST for Debian
=================

Since version 1.1, PyNAST no longer exactly matches the output
of the origianl NAST program. Instead it focuses on getting better
alignments. Users who wish to exactly match the results of NAST should
download PyNAST 1.0.

 -- Andreas Tille <tille@debian.org>  Tue, 29 Nov 2011 11:22:19 +0100

/usr/share/man/man1/pynast.1.gz

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
more»

/usr/share/doc/pynast/changelog.Debian.gz

python-pynast (1.1-3) unstable; urgency=low

  [ Steffen Moeller ]
  * Rendering Tim's fixes availab
more»

/usr/share/doc/pynast/changelog.gz

PyNAST 1.1 - (31 Mar 2010)
==========================
* Switch from BLAST for database search to ucl
more»

/usr/share/doc/pynast/copyright

Format: http://dep.debian.net/deps/dep5/
Upstream-Name: PyNAST
Upstream-Contact: Greg Caporaso <greg
more»

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