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Summary


XSTK is a suite of C and C++ libraries and command-line programs for DNA sequence analysis.  Tested on Mac OSX and a variety of Linux systems.


Includes source code for the following programs:


barcrawl -- Design barcoded oligonucleotides for multiplex sequencing.

bartab --  Annotate, bin and dereplicate barcoded DNA sequences.

biodiv -- Calculation of common ecological biodiversity indices.

minerna -- Extract rRNA sequences from GenBank file.

sortx -- OTU clustering of aligned sequences.

xscat -- Merge sequences in two fasta/q files.

xschim -- Create chimeric sequences.

xscrossout -- Post-process cross_match output.

xsdegap --  Remove gaps from fasta/q alignment file.

xsdstcmp -- Calculate distance matrix between two alignments.  Infers

                        taxonomy of query sequences from nearest match in first alignment.

xsel -- Select sequences from fasta/q file (use xsub to select subsequences).

xsqualgap -- Align quality scores with sequences in fasta format.

xsrep -- Dereplicate sequences in fasta/q file.

xsstat -- Collect basic statistics for sequences in fasta/q file.

xstrim -- Trim DNA sequences based on quality scores.

xsub -- Extract sub-alignment from multiple sequence alignment (fasta format).


Parsers:

fa2fq -- Translate from fasta to fastq format.

fa2nm -- List deflines in fasta file.

fa2nw -- Create newick-format selection tree from fasta file.

fa2qu --  Construct mock quality score file for fasta file.

fa2sto -- Translate from fasta to Stockholm format.

fq2fa -- Translate from fastq to fasta format.

gb2fa -- Translate from GenBank to fasta format.

nm2nw -- Create newick-format selection tree from list of taxon names.

si2fa -- Translate from SINA to fasta format.

sto2fa -- Translate from Stockholm to fasta format.

Download


By downloading this software you certify that you will use XSTK solely under the terms outlined in the license agreement.  Click on the link to download.  Once downloaded, double click the tar.gz file to uncompress.   Installation instructions are provided in the INSTALL file of the xstk directory.

Citation


For barcrawl and bartab:


Frank DN (2009) BARCRAWL and BARTAB: Software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics 10: 362.


All others:  Frank DN (2009) Personal communication.

Contact


Daniel N. Frank, Ph.D.  daniel(dot)frank at ucdenver(dot)edu

Copyright 1999-2011

XplorSeq ToolKit

Tools for nucleic acids sequence analysis

 xstk_30May2012.tar.gzXSTK_files/xstk_30May2012.tar.gzhttp://www.apple.com/shapeimage_3_link_0