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identify members of gene families.

FASTA includes:

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performs a rigorous Smith-Waterman alignment between a protein sequence
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identify members of gene families.

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ssearch
performs a rigorous Smith-Waterman alignment between a protein sequence
and another protein sequence or a protein database.
fastx/fasty
compare a DNA sequence to a protein sequence database, translating
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Debug information is useful when developing applications that use this
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  <description>This package provides debug information for package SHRiMP.
Debug information is useful when developing applications that use this
package or when debugging this package.</description>
  <packager/>
  <url>http://compbio.cs.toronto.edu/shrimp/</url>
  <time file="1305595010" build="1305594968"/>
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  <description>This package provides debug sources for package SHRiMP.
Debug sources are useful when developing applications that use this
package or when debugging this package.</description>
  <packager/>
  <url>http://compbio.cs.toronto.edu/shrimp/</url>
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  <description>This package provides debug sources for package SHRiMP.
Debug sources are useful when developing applications that use this
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  <packager/>
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  <description>ALLPATHS is a whole genome shotgun assembler that can generate high quality assemblies
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such as those arising from polymorphism, thereby providing information that has been
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    <file>/usr/bin/RunAllPaths3G</file>
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Both algorithms do gapped alignment. They are usually more accurate and faster on
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Debug information is useful when developing applications that use this
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  <description>This package provides debug information for package maqview.
Debug information is useful when developing applications that use this
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Debug sources are useful when developing applications that use this
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Debug sources are useful when developing applications that use this
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  <description>This package provides debug information for package muscle.
Debug information is useful when developing applications that use this
package or when debugging this package.</description>
  <packager/>
  <url>http://www.drive5.com/muscle</url>
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  <description>This package provides debug information for package muscle.
Debug information is useful when developing applications that use this
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  <url>http://www.drive5.com/muscle</url>
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  <description>Bio::Graphics::Panel - Generate GD images of Bio::Seq objects</description>
  <packager/>
  <url>http://search.cpan.org/dist/Inline-CPP/</url>
  <time file="1351852022" build="1351852008"/>
  <size package="590853" installed="1463883" archive="1501372"/>
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    <file>/usr/bin/contig_draw.pl</file>
    <file>/usr/bin/glyph_help.pl</file>
    <file>/usr/bin/search_overview.pl</file>
    <file>/usr/bin/frend.pl</file>

  </format>
</package>
<package type="rpm">
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  <description>Bio::Graphics::Panel - Generate GD images of Bio::Seq objects</description>
  <packager/>
  <url>http://search.cpan.org/dist/Inline-CPP/</url>
  <time file="1351852022" build="1351852008"/>
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  <description>Bio::Graphics::Panel - Generate GD images of Bio::Seq objects</description>
  <packager/>
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  <time file="1351852031" build="1351852017"/>
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hash and an object-oriented interfaces. It provides the ability to read fields from
SCF files and limited ability to modify them and write them back.</description>
  <packager/>
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  <summary>Debug sources for package samtools</summary>
  <description>This package provides debug sources for package samtools.
Debug sources are useful when developing applications that use this
package or when debugging this package.</description>
  <packager/>
  <url>http://samtools.sourceforge.net/</url>
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  <description>This package provides development files for SAM (Sequence Alignment/Map)
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SAM (Sequence Alignment/Map) format is a generic format for storing large
nucleotide sequence alignments.

SAM Tools provide various utilities for manipulating alignments in the SAM
format, including sorting, merging, indexing and generating alignments in
a per-position format.</description>
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  <description>This package provides development files for SAM (Sequence Alignment/Map)
Tools.

SAM (Sequence Alignment/Map) format is a generic format for storing large
nucleotide sequence alignments.

SAM Tools provide various utilities for manipulating alignments in the SAM
format, including sorting, merging, indexing and generating alignments in
a per-position format.</description>
  <packager/>
  <url>http://samtools.sourceforge.net/</url>
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  <description>SWAP454 is a program for calling SNPs using 454 read data. It aligns to the genome
using a novel alignment tool called QueryLookupTable, and looks for unique alignments
to a reference. Using those alignments, a coverage map file is built that indicates
the coverage and base calls for each base position on the reference. This coverage is
filtered using a neighborhood-quality score method. The coverage map file can be transformed
into individual SNP calls. SWAP454 also includes code for creating improved quality scores
for 454 read data that has been incorporated into the algorithm used by 454 Life Sciences.</description>
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  <url>http://www.broadinstitute.org/crd/wiki/index.php/SWAP454_Main_Page</url>
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  <description>SWAP454 is a program for calling SNPs using 454 read data. It aligns to the genome
using a novel alignment tool called QueryLookupTable, and looks for unique alignments
to a reference. Using those alignments, a coverage map file is built that indicates
the coverage and base calls for each base position on the reference. This coverage is
filtered using a neighborhood-quality score method. The coverage map file can be transformed
into individual SNP calls. SWAP454 also includes code for creating improved quality scores
for 454 read data that has been incorporated into the algorithm used by 454 Life Sciences.</description>
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aligner Bowtie, and then analyzes the mapping results to identify splice
junctions between exons.

TopHat is a collaborative effort between the University of Maryland Center
for Bioinformatics and Computational Biology and the University of California,
Berkeley Departments of Mathematics and Molecular and Cell Biology.</description>
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reads to mammalian-sized genomes using the ultra high-throughput short read
aligner Bowtie, and then analyzes the mapping results to identify splice
junctions between exons.

TopHat is a collaborative effort between the University of Maryland Center
for Bioinformatics and Computational Biology and the University of California,
Berkeley Departments of Mathematics and Molecular and Cell Biology.</description>
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TopHat is a collaborative effort between the University of Maryland Center
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Debug information is useful when developing applications that use this
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  <description>This package provides debug information for package tophat.
Debug information is useful when developing applications that use this
package or when debugging this package.</description>
  <packager/>
  <url>http://tophat.cbcb.umd.edu</url>
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    <file>/usr/lib/debug/usr/bin/sam_juncs.debug</file>
    <file>/usr/lib/debug/usr/bin/bam2fastx.debug</file>
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    <file>/usr/lib/debug/usr/bin/library_stats.debug</file>
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    <file>/usr/lib/debug/usr/bin/gtf_juncs.debug</file>
    <file>/usr/lib/debug/usr/bin/tophat_reports.debug</file>
    <file>/usr/lib/debug/usr/bin/segment_juncs.debug</file>
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  <description>This package provides debug sources for package tophat.
Debug sources are useful when developing applications that use this
package or when debugging this package.</description>
  <packager/>
  <url>http://tophat.cbcb.umd.edu</url>
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</package>
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  <description>This package provides debug sources for package tophat.
Debug sources are useful when developing applications that use this
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  <url>http://tophat.cbcb.umd.edu</url>
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  <description>VAAL is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex
genetic variants. On bacterial data sets, it achievies very high sensitivity, and near perfect
specificity. VAAL can be used to compare reads from one strain to a reference sequence from another
strain. It can also be used to compare reads from two strains to each other, using a third strain
to determine homology. For example, we have used VAAL to find a single mutation responsible for
bacterial resistance: the output of the program was that single mutation and no others.
VAAL uses an assisted assembly algorithm that borrows from ALLPATHS.</description>
  <packager/>
  <url>http://www.broadinstitute.org/crd/wiki/index.php/VAAL_Main_Page</url>
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  <description>VAAL is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex
genetic variants. On bacterial data sets, it achievies very high sensitivity, and near perfect
specificity. VAAL can be used to compare reads from one strain to a reference sequence from another
strain. It can also be used to compare reads from two strains to each other, using a third strain
to determine homology. For example, we have used VAAL to find a single mutation responsible for
bacterial resistance: the output of the program was that single mutation and no others.
VAAL uses an assisted assembly algorithm that borrows from ALLPATHS.</description>
  <packager/>
  <url>http://www.broadinstitute.org/crd/wiki/index.php/VAAL_Main_Page</url>
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    <file>/usr/bin/TruePoly</file>
    <file>/usr/bin/ImperfectLookupTable</file>
    <file>/usr/bin/VAAL4</file>
    <file>/usr/bin/MakeLookupTable</file>
    <file>/usr/bin/VAAL1_5</file>
    <file>/usr/bin/QueryLookupTable</file>
    <file>/usr/bin/ScaffoldAccuracy</file>
    <file>/usr/bin/Fastb</file>
    <file>/usr/bin/Qualb</file>
    <file>/usr/bin/VAAL0_5</file>
    <file>/usr/bin/VAAL</file>
    <file>/usr/bin/VAALCompareCompound</file>
    <file>/usr/bin/ShortQueryLookup</file>
    <file>/usr/bin/VAALrun</file>
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  <name>velvet</name>
  <arch>i586</arch>
  <version epoch="0" ver="1.0.19" rel="1.1"/>
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  <summary>Sequence assembler for very short reads</summary>
  <description>Velvet is a set of algorithms manipulating de Bruijn graphs for genomic Sequence assembly.
It was designed for short read sequencing technologies, such as Solexa or 454 Sequencing
and was developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute.

The tool takes in short read sequences, removes errors then produces high quality unique
contigs. It then uses paired-end read and long read information, when available, to retrieve
the repeated areas between contigs.</description>
  <packager/>
  <url>http://www.ebi.ac.uk/~zerbino/velvet/</url>
  <time file="1301057142" build="1301057125"/>
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  <description>Velvet is a set of algorithms manipulating de Bruijn graphs for genomic Sequence assembly.
It was designed for short read sequencing technologies, such as Solexa or 454 Sequencing
and was developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute.

The tool takes in short read sequences, removes errors then produces high quality unique
contigs. It then uses paired-end read and long read information, when available, to retrieve
the repeated areas between contigs.</description>
  <packager/>
  <url>http://www.ebi.ac.uk/~zerbino/velvet/</url>
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  <description>Velvet is a set of algorithms manipulating de Bruijn graphs for genomic Sequence assembly.
It was designed for short read sequencing technologies, such as Solexa or 454 Sequencing
and was developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute.

The tool takes in short read sequences, removes errors then produces high quality unique
contigs. It then uses paired-end read and long read information, when available, to retrieve
the repeated areas between contigs.</description>
  <packager/>
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Debug information is useful when developing applications that use this
package or when debugging this package.</description>
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  <description>This package provides debug information for package velvet.
Debug information is useful when developing applications that use this
package or when debugging this package.</description>
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