<h2>Lighter released</h2>
<ul>
   <li>Lighter is an extremely fast and memory-efficient program for correcting sequencing errors in DNA sequencing data.  For details on how error correction can help improve the speed and accuracy of downstream analysis tools, see the <a href="http://genomebiology.com/2014/15/11/509">paper in Genome Biology</a>.  Source and software <a href="https://github.com/mourisl/Lighter">available at GitHub</a>.
</ul>

<h2>1.1.1 - 10/1/2014</h2>
<ul>
   <li> Fixed a compiling linkage problem related with Mac OS X Mavericks.</li>
   <li> Improved performance for cases where the reference contains many stretches of Ns.</li>
   <li> Some minor automatic tests updates.</li>
</ul>


<h2>1.1.0 - 7/19/2014</h2>
<ul>
   <li> Added support for large and small indexes, removing 4-billion-nucleotide
     barrier.  Bowtie can now be used with reference genomes of any size.</li>
   <li> No longer releasing 32-bit binaries. Simplified manual and Makefile accordingly.</li>
   <li> Phased out CygWin support.</li>
   <li> Improved efficiency of index files loading.</li>
   <li> Fixed a bug that made <tt>bowtie-inspect</tt> fail in some situations.</li>
   <li> (This release was briefly given version number 2.0.0, but we changed it to 1.1.0
        to avoid confusion with Bowtie 2.)</li>
</ul>

<h2>1.0.1 release - 3/14/2014</h2>
<ul>
 <li>Improved index querying efficiency using "population count" instructions
     available since SSE4.2.</li>
 <li>Credits to the Intel(r) enabling team for performance optimizations
     included in this release.  Thank you!</li>
</ul>

<h2>Bowtie on GitHub - 4/11/13</h2>
<ul>
 <li>Bowtie source now lives in a <a href="https://github.com/BenLangmead/bowtie">public GitHub repository</a>.</li>
</ul>

<h2>1.0.0 release - 4/9/13</h2>
<ul>
 <li>Finally, a 64-bit Windows binary!</li>
 <li>Due to general performance improvements spinlocking 
     is now used by default. The <tt>EXTRA_FLAGS=-DNO_SPINLOCK</tt> may be 
     used to reverse this during compilation.</li>
 <li>Fixed some race conditions.</li>
 <li>CygWin builds now use pthreads library.</li>
 <li>Changed MinGW to optionally use pthread library on Win32 platforms.</li>
 <li>Changed the Windows build to use native Windows threads by default.</li>
 <li>Renamed <tt>COPYING</tt> to <tt>LICENSE</tt> to be more GitHub-friendly.</li>
 <li>Tokenizer no longer has limit of 10,000 tokens, which was a
     problem for users trying to index a very large number of FASTA
     files.</li>
 <li>Removed references to no-longer-implemented <tt>--cutoff</tt> option for
     bowtie-build</li>
</ul>

<h2>0.12.9 release - 12/16/12</h2>
<ul>
 <li>Fixed a bug whereby read names would not be truncated at first
     whitespace character in unmapped or maxed-out SAM records.</li>
 <li>Fixed errors and warnings when compiling with <tt>clang++</tt>.</li>
 <li>Fixed most errors and warnings when compiling with recent versions
     of <tt>g++</tt>, though you may need to add <tt>EXTRA_FLAGS=-Wno-enum-compare</tt>
     to avoid all warnings.</li>
</ul>

<h2>0.12.8 release - 5/6/12</h2>
<ul>
   <li>Fixed a bug that would sometimes cause an immediate segmentation
     fault in
     <tt><a href="manual.shtml#bowtie-options-sam">--sam</a></tt>
     mode.</li>
   <li>Fixed <tt>make_galGal3.sh</tt> script to not omit chromosome 25.</li>
   <li>Removed <tt>-B</tt> option from usage message for <tt>bowtie-build</tt>; that option
     is not implemented.</li>
   <li>Fixed issue that could cause Bowtie not to compile when
     <tt>BOWTIE_PTHREADS</tt> is left undefined and <tt>pthreads.h</tt> is not present.</li>
   <li>Elaborated documentation for
     <tt><a href="">-B/--offbase</a></tt> option to indicate that
     it only affects offsets in the default output mode, not in SAM
     mode.</li>
</ul>

<h2><a href="bowtie2">Bowtie 2</a> beta released - 10/16/2011</h2>
<ul>
  <li><a href="bowtie2">Bowtie 2</a> 2.0.0-beta2 is available now.</li>
  <li>Differences between <a href="bowtie2">Bowtie 2</a> and Bowtie 1 include:</li>
  <li>
    <ul>
      <li>For reads longer than about 50 bp Bowtie 2 is generally faster, more
          sensitive, and uses less memory than Bowtie 1.  For relatively short
          reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or more
          sensitive.</li>
      <li>Bowtie 2 supports gapped alignment with affine gap penalties. Number
          of gaps and gap lengths are not restricted, except by way of the
          configurable scoring scheme.  Bowtie 1 finds just ungapped
          alignments.</li>
      <li>Bowtie 2 supports
          <a href="bowtie2/manual.shtml#end-to-end-alignment-versus-local-alignment">local alignment</a>,
          which doesn't require reads to align end-to-end.  Local alignments
          might be "trimmed" ("soft clipped") at one or both extremes in a way
          that optimizes alignment score. Bowtie 2 also supports
          <a href="bowtie2/manual.shtml#end-to-end-alignment-versus-local-alignment">end-to-end alignment</a>
          which, like Bowtie 1, requires that the read align entirely.</li>
      <li>There is no upper limit on read length in Bowtie 2.  Bowtie 1 has an
          upper limit of around 1000 bp.</li>
      <li>Bowtie 2 allows alignments to
          <a href="bowtie2/manual.shtml#ambiguous-characters">overlap ambiguous characters</a>
          (e.g. <tt>N</tt>s) in the reference.  Bowtie 1 does not.</li>
      <li>Bowtie 2 does away with Bowtie 1's notion of alignment "stratum", and
          its distinction between "Maq-like" and "end-to-end" modes.  In Bowtie
          2 all alignments lie along a continuous spectrum of alignment scores
          where the
          <a href="bowtie2/manual.shtml#ambiguous-characters#scores-higher-more-similar">scoring scheme</a>,
          similar to
          <a href="http://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm">Needleman-Wunsch</a>
          and
          <a href="http://en.wikipedia.org/wiki/Smith_waterman">Smith-Waterman</a>.</li>
      <li>Bowtie 2's
          <a href="bowtie2/manual.shtml#aligning-pairs">paired-end alignment</a>
          is more flexible.  E.g. for pairs that do not align in a paired
          fashion, Bowtie 2 attempts to find unpaired alignments for each
          mate.</li>
      <li>Bowtie 2 does not align colorspace reads.</li>
    </ul>
  </li>
</ul>

<h2>Fixed chicken index - 7/19/2011</h2>
<ul>
  <li><b>The pre-built chicken genome available from this website was missing
      chr25</b>.  chr25_random was included, but chr25 was erroneously excluded.
      This is fixed as of today - the index files linked to from the sidebar
      now contains all chicken chromosomes.
</ul>

<h2>0.12.7 release - 9/7/10</h2>
<ul>
  <li> Fixes the all-gap reference sequence issue that was present in
     Bowtie 0.12.6.  Index files produced by <tt>bowtie-build</tt> 0.12.5 and
     earlier (back to 0.10.*) are compatible with <tt>bowtie</tt> 0.12.7.  Index
     files produced by <tt>bowtie-build</tt> 0.12.7 are backward compatible with
     <tt>bowtie</tt> 0.12.5 and earlier as long as the first reference sequence
     is not all-gaps (or, when colorspace indexes, as long as the first
     reference sequence has two consecutive ACGT characters in it
     somewhere).
  <li> Indexes where the first sequence consists of all gaps or other
     non-ACGT characters are not handled properly by Bowtie versions
     0.12.5 and older, but are handled properly by Bowtie 0.12.7.
  <li> REMOVED: bowtie-build's <tt>--old-reverse</tt> option; the old reverse-
     index scheme is again the default.  The new scheme is disabled
     pending further refinement.
</ul>

<h2>0.12.6 release - 8/29/10</h2>
<ul>
 <li>
     Modified <a href="manual.shtml#the-bowtie-inspect-index-inspector"><tt>bowtie-inspect</tt></a>'s default mode to use the bit-encoded
     reference portion of the index to reconstruct the reference
     sequence, rather than the ebwt portion.  This makes <a href="manual.shtml#the-bowtie-inspect-index-inspector"><tt>bowtie-inspect</tt></a>
     much faster and uses less memory, and the output for a colorspace
     index will now be in nucleotide space.  To get the behavior of the
     old default, use the new
     <a href="manual.shtml#bowtie-inspect-options-e"><tt>-e/--ebwt-ref</tt></a>
     option.
 <li>
     Fixed bug whereby SOLiD QV strings
     without a trailing space would fail to parse.
 <li>
     Moved to a new default way of building the reverse index.  Revert
     to the old behavior with <tt>bowtie-build</tt>'s new
     <tt>--old-reverse</tt>
     option.
     The new reverse index format is forward and backward compatible
     with `bowtie`, unless otherwise noted in a future version.
 <li>
     Fixed issue that would sometimes cause bowtie-build to crash when
     building a large index with a low <a href="manual.shtml#bowtie-build-options-o"><tt>--offrate</tt></a>.
 <li>
     Fixed build issue that would cause <tt>bowtie-build</tt> built on one version of
     Linux to die with a "floating point error" on other versions.
     bowtie now simply skips reads with 0 characters.  Previously it
     would print an error and exit.
 <li>
     Fixed a bug whereby alignment cost could sometimes be
     miscalculated.  Stratum was unaffected.
 <li>
     <tt>bowtie</tt> now simply skips reads with 0 characters.  Previously it
     would print an error and exit.
</ul>

<h2>Myrna paper out - 8/11/10</h2>
<ul>
 <li>
   The provisional version of the <a href="http://genomebiology.com/2010/11/8/R83/abstract">Myrna paper</a>
   appeared today in <a href="http://genomebiology.com/">Genome Biology</a>.  See the <a href="http://bowtie-bio.sourceforge.net/myrna">Myrna site</a>
   for details about the software.
</ul>

<h2>Myrna released - 7/22/10</h2>
<ul>
  <li><a href="myrna">Myrna</a> is cloud-scale tool for calculating differential gene
      expression in large RNA-seq datasets.  It is very similar to
      Crossbow in design and philosophy; e.g. it uses Bowtie, it's
      "tri-mode" (runs in the cloud or on a Hadoop cluster or a single
      computer), it has a <a href="myrna/ui.html">web-form-based GUI</a> for
      composing and submitting cloud jobs, and its cloud mode uses
      <a href="http://aws.amazon.com/elasticmapreduce/">Elastic MapReduce</a>.
</ul>

<h2>Major update to Crossbow - 7/22/10</h2>
<ul>
  <li><a href="crossbow">Crossbow</a> has received a major update to
      version 1.0.4.  New features:
  <ul>
   <li>New "tri-mode" design; Crossbow jobs can be run in the cloud
      (on <a href="http://aws.amazon.com/">Amazon AWS</a>),
      on a <a href="http://hadoop.apache.org/">Hadoop</a> cluster,
      or on a single computer, exploiting multiple processor cores
   <li>Added a <a href="crossbow/ui.html">web-form-based GUI</a> for composing and submitting cloud jobs.
   <li>Cloud version of Crossbow now runs on
       <a href="http://aws.amazon.com/elasticmapreduce/">Elastic MapReduce</a>
       (EMR) rather than directly on
       <a href="http://aws.amazon.com/ec2/">Elastic Compute Cloud</a> (EC2).
  </ul>
</ul>

<h2>Cufflinks paper out - 5/3/10</h2>
<ul>
  <li>The <a href="http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.1621.html#/">Cufflinks paper</a>,
  by <a href="http://www.cs.umd.edu/~cole/">Cole Trapnell</a> <i>et al</i> is out
  in <a href="http://www.nature.com/nbt/index.html">Nature Biotechnology</a>.
  See the supplement for a detailed discussion of the methods behind 
  <a href="http://cufflinks.cbcb.umd.edu/">Cufflinks</a>.
</ul>

<h2>0.12.5 release - 4/10/10</h2>
<ul>
 <li>Fixed spurious "Error while writing string output; not all
     characters written" errors in
     <a href="manual.shtml#bowtie-options-S"><tt>-S/--sam</tt></a>
     mode.
</ul>

<h2>0.12.4 release - 4/5/10</h2>
<ul>
 <li>Periods in read sequences are now treated as Ns instead of
     ignored.  This should help with some problems where Bowtie
     erroneously reports "Reads file contained a pattern with more than
     1024 quality values..." for data from recent versions of the
     Illumina GA pipeline.
 <li>Fixed a bug whereby some error and warning messages would be
     printed on top of each other in
     <a href="manual.shtml#bowtie-options-p"><tt>-p</tt>/<tt>--threads</tt></a>
     mode.
 <li>Chunk-exhaustion warnings messages are now suppressed when
     <a href="manual.shtml#bowtie-options-quiet"><tt>--quiet</tt></a>
     is specified.
 <li>Fixed small issue in quality decoding whereby no-confidence colors
     would incorrectly influence decoded quality of adjacent bases.
</ul>

<h2>0.12.3 release - 2/17/10</h2>
<ul>
 <li>Fixed a significant bug in
      <a href="manual.shtml#bowtie-options-C"><tt>-C</tt>/<tt>--color</tt></a>
     mode whereby quality values for SNP nucleotide positions are
     erroneously penalized.
 <li>Fixed a bug in
     <a href="manual.shtml#bowtie-options-S"><tt>-S/--sam</tt></a>
     mode whereby if whitespace occurred in the original read name, it would be
     printed in the QNAME field in violation of the SAM spec.  Bowtie
     now truncates read names at the first whitespace character before
     printing.
 <li>When input is FASTQ and
     <a href="manual.shtml#bowtie-options-C"><tt>-C</tt>/<tt>--color</tt></a>
     is enabled, Bowtie is now tolerant of output from FASTQ converters that
     include the primer base and where the quality string is one character
     shorter than the sequence string (due to the primer).  This fixes issues
     users have reported using output from BFAST's solid2fastq.
 <li>Added support for SOLiD-style <tt>_QV</tt> files, via the 
     <a href="manual.shtml#bowtie-options-Q"><tt>-Q/--quals</tt></a>,
     <a href="manual.shtml#bowtie-options-Q1"><tt>--Q1</tt></a> and
     <a href="manual.shtml#bowtie-options-Q2"><tt>--Q2</tt></a>
     options.  These options are used in combination with 
     <a href="manual.shtml#bowtie-options-C"><tt>-C</tt>/<tt>--color</tt></a>
     and
     <a href="manual.shtml#bowtie-options-f"><tt>-f</tt></a>
     to align parallel colorspace read/quality files without having
     to convert to FASTQ.
</ul>

<h2>0.12.2 release - 2/2/10</h2>
<ul>
 <li>When
     <a href="manual.shtml#bowtie-options-C"><tt>-C</tt>/<tt>--color</tt></a>
     is enabled, the default paired-end orientation is
     now
     <a href="manual.shtml#bowtie-options-ff"><tt>--ff</tt></a>,
     not
     <a href="manual.shtml#bowtie-options-fr"><tt>--fr</tt></a>.
     The new default fits typical SOLiD output.
 <li>Fixed a bug whereby very large reads could cause <tt>bowtie</tt> to crash
     in
     <a href="manual.shtml#bowtie-options-best"><tt>--best</tt></a>
     mode
 <li>After 0.12.1, some issues remained whereby <tt>bowtie</tt> would fail to
     trim the primer in colorspace (e.g. in
     <a href="manual.shtml#bowtie-options-c"><tt>-c</tt></a>
     mode).  All input modes should now have fully-functioning
     colorspace primer trimming.
 <li>Fixed a bug whereby decoded colorspace qualities could overflow
     and erroneously become low qualities.
 <li>Fixed a bug that could produce incorrect paired-end alignment
     results in
     <a href="manual.shtml#bowtie-options-n"><tt>-n</tt></a>
     mode when using paired-end orientation modes other than
     <a href="manual.shtml#bowtie-options-fr"><tt>--fr</tt></a>
     Even with the bug, reported results are reasonable;
     but the seed edit constraint (
     <a href="manual.shtml#bowtie-options-n"><tt>-n</tt></a>
     ) may have been applied to the wrong end of one of the mates.
 <li>Changed
     <a href="manual.shtml#bowtie-options-chunkmbs"><tt>--chunkmbs</tt></a>
     default up to 64 from 32.
 <li>Better error checking and reporting for some <tt>bowtie</tt> options.
 <li>Some basic testing scripts are now bundled with Bowtie (in
     <tt>scripts/test</tt>), which should make it easier to regression-test.
</ul>

<h2>Fixed mm9 colorspace index</h2>
<ul>
 <li>Previously posted version of the colorspace
     <a href="http://hgdownload.cse.ucsc.edu/downloads.html#mouse">mm9</a>
     index was not actually colorspace.  This has been fixed.</li>
</ul>

<h2>0.12.1 release - 1/8/10</h2>
<ul>
 <li>IMPORTANT: Fixed bug whereby bowtie would fail to remove both the
     primer base and the first color when parsing .csfasta files with
     primer bases in
     <a href="manual.shtml#bowtie-options-C"><tt>-C</tt></a>
     <a href="manual.shtml#bowtie-options-f"><tt>-f</tt></a>
     mode.  A workaround for users of version
     0.12.0 is to use
     <a href="manual.shtml#bowtie-options-5"><tt>-5</tt></a>
     <tt>1</tt>
     in that situation.
 <li>Fixed bug whereby, when
     <a href="manual.shtml#bowtie-options-M"><tt>-M</tt></a> limit was
     exceeded for an unpaired read, the number output in the <a href="manual.shtml#default-bowtie-output">7th column</a>
     (or the
     <a href="manual.shtml#sam-bowtie-output"><tt>XM:i</tt></a>
     optional field)
     for the randomly-selected alignment was too low by 1.
 <li>Added
     <a href="manual.shtml#paired-end-colorspace-alignment">discussion</a>
     to manual about a pitfall regarding SOLiD paired-end input, i.e., not
     all entries necessarily have corresponding mates in the other file.
</ul>

<h2>0.12.0 release - 12/23/09</h2>
<ul>
 <li>Added missing <tt>README.markdown</tt> file
 <li>Minor documentation additions
</ul>

<h2>0.12.0-beta1 release - 12/15/09</h2>
<ul>
 <li>Added SOLiD colorspace support
 <ul>
  <li>Colorspace indexes are distinct from standard letterspace
      indexes and must be built with a separate invocation of
      bowtie-build (with <a href="manual.shtml#bowtie-options-C"><tt>-C</tt></a> option)
  <li>Running bowtie with <a href="manual.shtml#bowtie-options-C"><tt>-C</tt></a> causes Bowtie to align in colorspace.
      Both index and reads must be in colorspace.
  <li>Colorspace memory requirement is the same as paired-end alignment in
      letterspace (normal) mode.  Paired-end alignment does not increase the
      memory requirement further in colorspace.
  <li><tt>csfasta</tt>, <tt>csfastq</tt>, and "raw" read formats are all supported with
      <a href="manual.shtml#bowtie-options-C"><tt>-C</tt></a>.  In read sequences, <tt>0</tt> means "blue" and is intechangeable with
      <tt>A</tt>, likewise <tt>1</tt> (<tt>C</tt>) means "green",
      <tt>2</tt> (<tt>G</tt>) means "orange" and <tt>3</tt>
      (<tt>T</tt>) means "red".
  <li>Colorspace versions of indexes added (see sidebar)
  <li>New manual section discussing <a href="manual.shtml#colorspace-alignment">colorspace features</a>
 </ul>
 <li>Fixed a few SAM output issues
 <ul>
  <li><tt>@PG</tt> line now properly uses colons instead of equals signs
  <li>Removed <tt>/1</tt>, <tt>/2</tt> suffixes for paired-end reads in SAM mode
  <li>Added <a href="manual.shtml#bowtie-options-sam-RG"><tt>--sam-RG</tt></a> option that permits the user to insert set values
      for flags that appear on the <tt>@RG</tt> line
 </ul>
 <li>Fixed lingering pthreads bugs that could cause Bowtie to hang or
     crash toward the end of execution with <a href="manual.shtml#bowtie-options-p"><tt>-p</tt></a> > 1.
 <li>Fixed performance-related bug that would cause paired-end
     alignment to be artificially slow in many situations.
 <li>Fixed issue with random number generation that would result in
     non-random selection of alignments in some situations.
 <li><tt>bowtie -f</tt> now supports fasta files with reads split across
     multiple lines 
 <li>New <a href="manual.shtml#bowtie-options-suppress"><tt>--suppress</tt></a> option suppresses unwanted columns of output
 <li>The <tt>MANUAL</tt> file was converted to <a href="http://daringfireball.net/projects/markdown/syntax">markdown</a> format, facilitating
     conversion to various other formats using tools like <a href="http://johnmacfarlane.net/pandoc/">pandoc</a>
 <li><b>Deprecated</b>: <tt>bowtie</tt>: <tt>--concise</tt>, <tt>bowtie-build</tt>: <tt>--big</tt>, <tt>--little</tt>
 <li><b>Removed</b>: <tt>-z/--phased</tt>, <tt>-b/--binout</tt>, <tt>bowtie-maptool</tt>,
     <tt>bowtie-maqconvert</tt>
</ul>

<h2>Crossbow paper out - 11/20/09</h2>
<ul>
 <li>
   The provisional version of the <a href="http://genomebiology.com/2009/10/11/R134">Crossbow paper</a>
   appeared today in <a href="http://genomebiology.com/">Genome Biology</a>.
</ul>

<h2>New pre-built index list - 11/14/09</h2>
<ul>
  <li>The roster of pre-built indexes has been changed to address a number
      of user requests and issues and to streamline maintenance.
      Now:
  <ul>
    <li>All indexes are for well known assemblies.  Contig indexes have been removed.</li>
    <li>Indexes for UCSC builds <a href="http://hgdownload.cse.ucsc.edu/downloads.html#human">hg18</a>, <a href="http://hgdownload.cse.ucsc.edu/downloads.html#human">hg19</a> and <a href="http://hgdownload.cse.ucsc.edu/downloads.html#mouse">mm9</a> have been added.</li>
    <li>Rarely used indexes (chimp, rat, dog, chicken) have been removed.</li>
  </ul>
  <li>If there is an index not on the list that you use on a regular basis
      and would like to be made availble pre-built, contact us.
      We may add more if enough users request them.
  <li>Note: neither UCSC nor NCBI indexes contain unplaced contigs (UCSC:
      "random" files, NCBI: Chromosome "Un") or alternative haplotype
      assemblies.
</ul>

<h2>Bowtie on Galaxy - 10/15/09</h2>
<ul>
  <li>The <a href="http://main.g2.bx.psu.edu/">Galaxy project</a> has
      integrated Bowtie as one of the tools available for aligning short
      reads (under "NGS: Mapping" on in the "Tools" box).  Many thanks to
      Anton Nekrutenko for his work on that.
</ul>


<h2>0.11.3 release - 10/12/09</h2>
<ul>
   <li>Fixed crashing bug in <a href="manual.shtml#bowtie-options-S"><tt>-S/--sam</tt></a> mode when the number of reference
     sequences in the index is very large.
   <li>Added <a href="manual.shtml#bowtie-options-sam-nohead"><tt>--sam-nohead</tt></a> option to suppress output of SAM headers in
     <a href="manual.shtml#bowtie-options-S"><tt>-S/--sam</a></tt> mode.
   <li>Added <a href="manual.shtml#bowtie-options-sam-nosq"><tt>--sam-nosq</tt></a> option to suppress output of <tt>@SQ</tt> SAM headers in
     <a href="manual.shtml#bowtie-options-S"><tt>-S/--sam</a></tt> mode.  These can become a nuisance when the reference
     index contains a very large number of sequences.
   <li>Fixed a bug in <tt>bowtie-build</tt>'s auto-configure mode that would cause
     it to underestimate the amount of memory required by a set of
     parameters.  This in turn would cause the index to be corrupted.
</ul>

<h2>Crossbow released - 10/9/09</h2>
<ul>
   <li><a href="./crossbow">Crossbow</a> is a cloud-computing pipeline for whole genome resequencing. 
  It combines Bowtie and <a href="http://soap.genomics.org.cn/soapsnp.html">SoapSNP</a>, an accurate
  genotyper, on top of <a href="http://hadoop.apache.org">Hadoop</a>.  Crossbow includes scripts that
  run automatically on <a href="http://aws.amazon.com">Amazon's EC2 utility computing
  service</a> for a fee, allowing researchers without extravagant computing resources to conduct
  large experiments efficiently.  Authors are <a href="http://faculty.jhsph.edu/default.cfm?faculty_id=2209&grouped=false&searchText=&department_id=3&departmentName=Biostatistics">Ben Langmead</a> and <a href="http://www.cbcb.umd.edu/~mschatz/">Michael C. Schatz</a>.
</ul>

<h2>0.11.2 release - 10/7/09</h2>
<ul>
   <li>Fixed issue whereby <tt>--max</tt> option was disabled.
</ul>


<h2>0.11.1 mini-release - 10/5/09</h2>
<ul>
   <li>SAM output: changed <tt>XS:i</tt> optional field to be named
       <tt>XA:i</tt> to avoid a conflict with TopHat's <tt>XS:i</tt> field.
</ul>

<h2>0.11.0 release - 10/5/09</h2>
<ul>
   <li>Initial <a href="http://samtools.sf.net">SAM</a> output support with
   <a href="manual.shtml#bowtie-options-S"><tt>-S/--sam</tt></a>
   option.  <tt>bowtie</tt> sets all
     fields according to the <a href="http://samtools.sourceforge.net/SAM1.pdf">SAM spec</a> (Version 0.1.2-draft, 20090820).
     See the new
     <a href="manual.shtml#sam-bowtie-output">SAM Output</a>
     section of the manual for details.
   <li>The <a href="tutorial.shtml">Getting Started Guide</a> and <tt>TUTORIAL</tt> file have been updated to
     use <a href="http://samtools.sf.net">SAMtools</a> instead of <a href="http://maq.sf.net">Maq</a> for the SNP calling step.
   <li>Added
     <a href="manual.shtml#bowtie-options-shmem"><tt>--shmem</tt></a>
     option:
     <a href="manual.shtml#bowtie-options-shmem"><tt>--shmem</tt></a>
     is similar to
     <a href="manual.shtml#bowtie-options-mm"><tt>--mm</tt></a>
     in that it allows
     concurrent <tt>bowtie</tt> processes querying the same index to share a
     single memory image of the index.  Unlike
     <a href="manual.shtml#bowtie-options-mm"><tt>--mm</tt></a>,
     shared memory
     alocated by
     <a href="manual.shtml#bowtie-options-shmem"><tt>--shmem</tt></a> is permanent.
   <li>The alignment summary printed to stderr at the end of an alignment
     run is now more friendly and includes data about the number and
     proportion of reads that aligned, failed to align, or were
     suppressed via the
     <a href="manual.shtml#bowtie-options-m"><tt>-m</tt></a>
     option.
   <li>When too-short reads are encountered, <tt>bowtie</tt> now always prints
     warnings, not errors.
     <a href="manual.shtml#bowtie-options-quiet"><tt>--quiet</tt></a>
     now suppresses those warnings.
   <li>By default, when <tt>bowtie</tt> prints a reference sequence name it now
     stops at the first whitespace.  In 0.10.1, the default was to
     print the entire name, which could cause confusion when parsing
     <tt>bowtie</tt> output.  To revert to printing the full name, use the new
     <a href="manual.shtml#bowtie-options-fullref"><tt>--fullref</tt></a>
     option.
   <li><tt>bowtie</tt> now prints the command-line before exiting with an error.
   <li>Fixed mistake in the manual's "Default output" section: the offset
     in field 4 is 0-based, not 1-based.  To obtain a 1-based offset
     instead, use the <tt>-B 1</tt> option.
   <li>Various minor bug fixes.
   <li><b>Deprecated</b>: <tt>-z/--phased</tt>, <tt>-b/--binout</tt>, <tt>bowtie-maptool</tt>,
     <tt>bowtie-maqconvert</tt>.  These features will be removed in a future
     version of Bowtie.  Note that <tt>-b/--binout</tt>, <tt>bowtie-maptool</tt>, and
     <tt>bowtie-maqconvert</tt> are largely superseded by the SAM output format
     (<a href="manual.shtml#bowtie-options-S"><tt>-S/--sam</tt></a>), BAM, and <a href="http://samtools.sf.net">SAMtools</a>.  Contact
     the authors if this is a problem.
   <li><b>Removed</b>: <tt>--unfq/--unfa/--maxfq/--maxfa/--alfq/--alfa</tt>.  Please use
     <tt>--un/--max/--al</tt> instead.  Contact the authors if this is a
     problem.
</ul>

<h2>Cufflinks released - 9/28/09</h2>
<ul>
   <li><a href="http://cufflinks.cbcb.umd.edu/">Cufflinks</a>, a tool that assembles transcripts and estimates their
       abundances in RNA-Seq samples was released today.  The author is
       Cole Trapnell, who is also the author of <a href="http://tophat.cbcb.umd.edu/">TopHat</a>.</li>
</ul>


<h2>10,000 downloads - 9/21/09</h2>
<ul>
   <li>Since the first version was released a little over a year ago,
       Bowtie has been downloaded more than 10,000 times.  Our sincere
       thanks to users whose bug reports, suggestions and help have
       made this possible.  Thank you!</li>
</ul>

<h2>New human index - 8/26/09</h2>
<ul>
   <li>Added index files for NCBI 37.1 assembly.</li>
</ul>


<h2>New cow index - 8/26/09</h2>
<ul>
   <li>Added index files for the 3.0 version of the University of
       Maryland <i>Bos Taurus</i> (cow) assembly.  See sidebar.</li>
</ul>

<h2>0.10.1 release - 7/19/09</h2>
<ul>
   <li>Now when <tt><a href="manual.shtml#bowtie-options-3">-3/-5</a></tt>
     are used in combination with
     <tt><a href="manual.shtml#bowtie-options-I">-I/-X</a></tt>, the
     <tt><a href="manual.shtml#bowtie-options-I">-I/-X</a></tt>
     constraints are interpreted as applying to the original insert,
     not the trimmed insert.
   <li>Fixed issue whereby
    <tt><a href="manual.shtml#bowtie-options-I">-I</a></tt>
    option was ignored;
    <tt><a href="manual.shtml#bowtie-options-I">-I</a></tt> option works now.
   <li>Fixed a bug whereby some large indexes were incorrectly reported
     as corrupt by bowtie-build.
   <li>Fixed issue whereby negative quality values were wrongly rejected
     when both
     <tt><a href="manual.shtml#bowtie-options-integer-quals">--integer-quals</a></tt>
     and
     <tt><a href="manual.shtml#bowtie-options-solexa-quals">--solexa-quals</a></tt>
     were specified.
   <li>The
     <tt><a href="manual.shtml#bowtie-options-l">-l/--seedlen</a></tt>
     parameter can now be adjusted down to 5 (previously had to be >= 20).
   <li>Fixed several minor memory leaks and out-of-bounds issues.  The
     Linux version of the <tt>bowtie</tt> aligner now receives a clean bill of
     health from
     <a href="http://valgrind.org/">valgrind's</a>
     <a href="http://valgrind.org/docs/manual/mc-manual.html">memcheck</a>.
   <li>Other minor bugfixes.
</ul>

<h2>0.10.0.2 release - 6/28/09</h2>
<ul>
   <li>Second bugfix for Windows version.  <tt>src</tt> and
   <tt>bin-win32</tt> packages updated.  Linux and Mac users are not
   affected.  Thanks for your bug reports and patience.
</ul>
<br/>

<h2>0.10.0.1 release - 6/23/09</h2>
<ul>
   <li>Fix for crashing bug in Windows version.  <tt>src</tt> and
   <tt>bin-win32</tt> packages updated.  Linux and Mac users are not
   affected.
</ul>
<br/>

<h2>Note to TopHat users</h2>
<ul>
   <li><a href="http://tophat.cbcb.umd.edu">TopHat</a> is not yet
   compatible with Bowtie 0.10.0.  Stay tuned to the
   <a href="http://tophat.cbcb.umd.edu">TopHat site</a> for updated
   information on <a href="http://tophat.cbcb.umd.edu">TopHat</a>/Bowtie
   0.10.0 compatibility.
</ul>
<br/>

<h2>0.10.0 release - 6/15/09</h2>
<ul>
   <li>Major change: All alignment modes are now unstratified by default.
     The <tt>--nostrata</tt> option has been removed, since it is now the
     default.  A
     <a href="manual.shtml#bowtie-options-strata"><tt>--strata</tt></a>
     option has been added to override the default
     and force stratified reporting.  Reporting is stratified if and
     only if
     <a href="manual.shtml#bowtie-options-strata"><tt>--strata</tt></a> is specified.
     <a href="manual.shtml#bowtie-options-strata"><tt>--strata</tt></a> now cannot be specified
     without also specifying <a href="manual.shtml#bowtie-options-best"><tt>--best</tt></a>.  
     Please note that, because of this
     change, specifying the same arguments to this version of Bowtie
     may yield different reported results.
   <li>Replaced the <tt>--unfa/--unfq</tt> options with a single
     <a href="manual.shtml#bowtie-options-un"><tt>--un</tt></a> option,
     which writes unaligned reads to an output file (or pair of output
     files) but keeps reads in their original form.  This is in
     contrast to the old <tt>--unfa/--unfq</tt> options, which only supported
     FASTA or FASTQ formats, and which would print a post-trimming and
     post-quality-value translation version of the read.  Likewise, the
     <tt>--alfa/--alfq</tt> and <tt>--maxfa/--maxfq</tt> options have been replaced with
     <a href="manual.shtml#bowtie-options-al"><tt>--al</tt></a>
     and <a href="manual.shtml#bowtie-options-max">
     <tt>--max</tt></a> options.  The old options are still present, but
     are deprecated and will be removed in a future version.
   <li>Added <a href="manual.shtml#bowtie-options-nofw"><tt>--nofw</tt></a>
     and <a href="manual.shtml#bowtie-options-norc"><tt>--norc</tt></a> options, allowing
     alignment to just one reference strand or the other.
   <li>Added <a href="manual.shtml#bowtie-options-mm"><tt>--mm</tt></a> option that causes <tt>bowtie</tt> to use memory-mapped files
     instead of traditional file I/O to access the reference index.
     This allows multiple <tt>bowtie</tt> processes running on the same computer
     to share a single in-memory image of a given index.  This is a
     useful feature for parallelizing <tt>bowtie</tt> in situations where memory
     is limited and where <a href="manual.shtml#bowtie-options-p">-p</a> is inappropriate or insufficient.
     This feature is not available in the Windows version of Bowtie.
   <li>Added a section to the manual (&quot;<a href="manual.shtml#reporting-modes">Reporting Modes</a>&quot;) clarifying and
     giving examples of how to use Bowtie's reporting options.
   <li>The <a href="manual.shtml#bowtie-options-al"><tt>--al</tt></a> and <tt>-z/--phased</tt> options previously interacted in such a
     way that the <a href="manual.shtml#bowtie-options-al"><tt>--al</tt></a> file could contain multiple entries for the same
     aligned read.  <a href="manual.shtml#bowtie-options-al"><tt>--al</tt></a> and <tt>-z/--phased</tt> are now incompatible.
   <li>The <tt>--oldpmap</tt> option, deprecated in version 0.9.8, has been
     removed.
</ul>
<br/>

<h2>0.9.9.3 release - 5/12/09</h2>
<ul>
   <li>Fixed an issue where <a href="manual.shtml#bowtie-options-best"><tt>bowtie --best</tt></a> would sometimes use excessive
     amounts of memory to store path descriptors.  There is now a per-thread
     32-MB ceiling (configurable with new option <a href="manual.shtml#bowtie-options-chunkmbs"><tt>--chunkmbs &lt;int&gt;</tt></a>)
     on the memory taken by path descriptors.  If the ceiling is
     exceeded Bowtie will skip the offending read, print a warning
     message identifying the read, and continue.
   <li>More options are available for defining the quality-value format,
     including new <a href="manual.shtml#bowtie-options-phred64-quals"><tt nowrap>--phred64-quals</tt>/<tt nowrap>--solexa1.3-quals</tt></a> options
     appropriate for the 64-based-Phred output of Illumina's GA
     Pipeline 1.3.  Added option <a href="manual.shtml#bowtie-options-phred33-quals"><tt nowrap>--phred33-quals</tt></a> to to handle the more
     typical 33-based-Phred scale (the default).  The <a href="manual.shtml#bowtie-options-solexa-quals"><tt nowrap>--solexa-quals</tt></a>
     option still handles the 64-based-Solexa scale output by GA
     Pipeline versions prior to 1.3.
   <li><tt>bowtie-build</tt> now checks output files for obvious corruption due,
     for example, to disk exhaustion.
   <li>Specifying <tt>-</tt> (meaning <tt>stdin</tt>) as an input to <tt>bowtie</tt> is now
     supported and documented.
   <li>Fixed a bug whereby <tt nowrap>bowtie-maqconvert</tt> could fail to notice that it
     had exhausted memory and output a corrupt Maq map file.
   <li>Fixed a bug whereby <tt>bowtie</tt> would crash when trying to use an index
     built on a machine with different endianness.
   <li>Fixed several issues that prevented Bowtie from compiling on
     Solaris.  I confirm that Bowtie builds and runs on Solaris 10.
   <li>Added <tt>_LARGEFILE_SOURCE _FILE_OFFSET_BITS=64 _GNU_SOURCE</tt> to the
     default build options in an attempt to resolve some of the large-file
     issues users are having.
   <li>Clarified column 7 in the manual.  We received many queries from
     users curious about this number.
   <li>Moderate speed improvements in <a href="manual.shtml#bowtie-options-best"><tt>--best</tt></a> mode.
</ul>
<br/>

<h2>0.9.9.2 release - 4/6/09</h2>
<ul>
   <li>Paired-end alignment is now available in all alignment modes,
     including all <a href="manual.shtml#bowtie-options-n"><tt>-n</tt></a> modes.
   <li><a href="manual.shtml#bowtie-options-best"><tt>--best</tt></a> now provides better guarantees.  Reported alignments are
     now guaranteed to be "best" both in terms of stratum (i.e. number of
     mismatches, or mismatches in the seed in the case of <a href="manual.shtml#bowtie-options-n"><tt>-n</tt></a> mode),
     and in terms of the quality values at the mismatched position(s).
     Stratum always trumps quality when determining best alignments.
     Also, <a href="manual.shtml#bowtie-options-best"><tt>--best</tt></a> mode resolves the strand bias issue that is present
     in the default mode (see manual
     for a discussion of the issue).
   <li>Speed improvements for <tt>--best</tt> mode in most alignment modes.
   <li>Major speed improvement for the <a href="manual.shtml#bowtie-options-v"><tt>-v 3</tt></a> alignment mode (except when <tt>-z</tt> is also used).
   <li>The "Reported X alignments..." message is now printed to stderr
     rather than stdout.  Only alignments are written to stdout.
   <li>In <tt>bowtie-maqconvert</tt>, read names longer than Maq's limit (36) are now
     truncated to a suffix of the original name, rather than a prefix.
     This mimics Maq's behavior and prevents <tt>/1</tt> and <tt>/2</tt> suffixes for
     paired-end reads from being destroyed.
   <li>Added <tt>--alfq/--alfa</tt> options to dump aligned reads to FASTQ and/or
     FASTA files.</li>
   <li>Removed many extraneous source files.</li>
</ul>
<br/>

<h2>TopHat paper out - 3/17/09</h2>
<ul>
  <li>The <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp120">TopHat paper</a>,
  by <a href="http://www.cs.umd.edu/~cole/">Cole Trapnell</a>, <a href="http://math.berkeley.edu/~lpachter/">Lior Pachter</a>, and <a href="http://www.cbcb.umd.edu/~salzberg/">Steven L. Salzberg</a> is out
  in <a href="http://bioinformatics.oxfordjournals.org/">Bioinformatics</a>
  advance access.</li>
</ul>
<br/>
<h2>0.9.9.1 release - 3/11/09</h2>
<ul>
   <li>Added paired-end alignment for <tt>-v 2</tt> and <tt>-v 3</tt> alignment modes (<tt>-n</tt>
     modes coming soon).</li>
   <li>Minor bug fixes and speed improvements for all paired-end modes.</li>
   <li>Added <a href="manual.shtml#bowtie-options-s"><tt>-s/--skip &lt;int&gt;</tt></a> option to skip over the first <tt>&lt;int&gt;</tt> reads or
     pairs in the input.</li>
   <li><tt>--unfq/--unfa/--maxfq/--maxfa</tt> modes no longer create empty output
     files. </li>
   <li>All Bowtie tools now compile under GCC 4.3.3.</li>
   <li>Fixed bug whereby <tt>bowtie -b</tt> would sometimes write garbage into the
     reference offset field.</li>
   <li>Paired-end info is now persisted in the <tt>-b</tt> format, allowing
     <tt>bowtie-maptool</tt> output to add <tt>/1</tt> and <tt>/2</tt> suffixes as
     appropriate.</li>
</ul>
<br/>
<h2>Final paper out - 3/10/09</h2>
<ul>
   <li>The <a href="http://genomebiology.com/2009/10/3/R25">Bowtie paper</a>
   in <a href="http://genomebiology.com">Genome Biology</a> is now final.
</ul>
<br/>
<h2>0.9.9 release - 2/19/09</h2>
<ul>
   <li>Added some preliminary support for paired-end alignment in <a href="manual.shtml#bowtie-options-v"><tt>-v 0</tt></a>
     and <a href="manual.shtml#bowtie-options-v"><tt>-v 1</tt></a> modes.  <a href="manual.shtml#command-line-1"><tt>-1</tt></a>/<a href="manual.shtml#command-line-1"><tt>-2</tt></a> options to specify the paired-end files,
     <a href="manual.shtml#bowtie-options-I"><tt>-I</tt></a>/<a href="manual.shtml#bowtie-options-I"><tt>-X</tt></a> to specify min and max insert sizes, and <a href="manual.shtml#bowtie-options-fr"><tt>--fr</tt>/<tt>--rf</tt>/<tt>--ff</tt></a>
     specify relative orientation of upstream and downstream mates.
     bowtie-build now builds two additional files: <tt>NAME.3.ebwt</tt> and
     <tt>NAME.4.ebwt</tt>.  Together, these files store a bitpacked version of
     the reference and they are required for paired-end alignment.  If
     your index does not include these files and you would like to
     perform a paired-end alignment, you will have to rebuild the index
     with <tt>bowtie-build</tt> version 0.9.9 or later.  Paired-end alignment is
     not compatible with <tt>-z</tt> mode, and it incurs about a 30% greater
     memory overhead than single-end mode.
   <li>Pre-built indexes available from Bowtie website have been updated
     to include <tt>.3</tt>/<tt>.4.ebwt</tt> index files.  These new pre-built indexes
     are no longer compatible with bowtie versions prior to 0.9.8.
   <li>New <a href="manual.shtml#bowtie-options-B"><tt>-B</tt>/<tt>--offbase</tt></a> option allows user to specify how bowtie numbers
     reference positions in its output.  E.g. <tt>-B 1</tt> causes bowtie to
     number leftmost char as 1.  <tt>-B 0</tt> is the default, but <tt>-B 1</tt> will
     likely become the default in the 1.0 release.
   <li>Fixed a bug that caused trimming options <a href="manual.shtml#bowtie-options-3"><tt>-3</tt></a> and <a href="manual.shtml#bowtie-options-5"><tt>-5</tt></a> not to work
     properly in <a href="manual.shtml#bowtie-options-r"><tt>-r</tt></a> (raw input) mode.
   <li><tt>bowtie-build</tt> now prints a friendly error message and exits if an
     input file doesn't exist.
   <li>Fixed a bug that caused the Win32 version of <tt>bowtie</tt> to hang just
     before it would normally have exited.
   <li>Fixed bug that could prevent successful read-in of very large
     (>1GB) <tt>.2.ebwt</tt> index files.
   <li>Removed <tt>--maxns</tt> option since it's mostly redundant with what <tt>-v</tt>
     and <tt>-n</tt> already do.
   <li>Removed <tt>--ntoa</tt> option.
   <li><tt>bowtie</tt> usage message is now divided into sections for clarity.
 </ul>
  <br/>

<h2>Added AGBT poster - 2/5/09</h2>
 <ul>
   <li>...to Other Documentation section in the right-hand sidebar</li>
 </ul>
 <br/>

<h2>Paper coming soon - 1/27/09</h2>
 <ul>
   <li>Bowtie paper <i>Ultrafast and memory-efficient alignment of short DNA sequences
   to the human genome</i> is accepted at <a href="http://genomebiology.com">Genome Biology</a>.
   A link to the paper will be posted when available.</li>
   <li>Added Related Tools, Publications, Other Documentation sections to right-hand sidebar.</li>
 </ul>
 <br/>
<h2>Paper out - 3/4/09</h2>
<ul>
   <li>The <a href="http://genomebiology.com/2009/10/3/R25">provisional PDF</a> of our paper <i>Ultrafast and
   memory-efficient alignment of short DNA sequences to the human genome</i>
   is available at <a href="http://genomebiology.com">Genome Biology</a>.
</ul>
<br/>
<h2>Current goals - 3/4/09</h2>
<ul>
   <li>Current goals in rough order of priority are:</li>
   <ul>
     <li>Expanding preliminary paired-end support (new in 0.9.9) into full paired-end support.</li>
     <li>Better alignment guarantees.</li>
     <li>Gapped alignment.</li>
   </ul>
   <li>Also of interest: colorspace support and mapping qualities.</li>
</ul>
<br/>
<h2>0.9.8.1 release - 1/7/09</h2>
 <ul>
 <li>Fixed all known problems with the <tt>--unfa/--unfq</tt> options:</li>
  <ul>
  <li>They now work properly with multiple threads.</li>
  <li>Fixed issue where sequence and quals were sometimes reversed.</li>
  <li>Fixed other issues causing spurious omission of unaligned reads.</li>
  </ul>
 <li>Added <tt>--maxfa/--maxfq</tt> options so that reads that don't align due
 to the -m limit can be dumped separately from reads that don't
 align at all.</li>
 <li>Alignment output is now guaranteed to be "deterministic" even when
 multiple threads are used.  I.e., given the same input reads (in
 any order) and the same <a href="manual.shtml#bowtie-options-seed"><tt>--seed</tt></a>, <tt>bowtie</tt> will produce the same
 alignments every time it is run, though not necessarily in the
 same order.  This does not hold across different versions of
 Bowtie.</li>
 <li>Multiple other bug fixes.</li>
 </ul>
  <br/>
<h2>0.9.7 release - 11/8/08</h2>
  <ul>
  <li>Added new reporting option <a href="manual.shtml#bowtie-options-m"><tt>-m &lt;int&gt;</tt></a> which suppresses all
 	alignments for a particular read if more than <tt>&lt;int&gt;</tt> reportable
 	alignments exist for it.</li>
  <li>Threads now buffer all alignments for a particular read/phase then
 output all alignments in one critical section.  This guarantees
 that all alignments for a given read/phase appear in one
 consecutive block of the output, even when multiple threads are
 operating in parallel. </li>
 <li>Separated the quality-conversion and parsing aspects of the old
 <tt>--solexa-quals</tt> argument into separate arguments: <a href="manual.shtml#bowtie-options-solexa-quals"><tt>--solexa-quals</tt></a>
 (quality conversion) and <a href="manual.shtml#bowtie-options-integer-quals"><tt>--integer-quals</tt></a> (parsing).</li>
 <li>bowtie-convert now handles the new (post-0.7.0) Maq alignment
 format.  The new format allows Maq tools to handle reads up to
 127 bases, whereas the old format was limited to 63 bases.  Added
 a -o option to opt for the old Maq format.</li> 
 <li>New <a href="manual.shtml#bowtie-options-refout"><tt>--refout</tt></a> argument sends alignments to a set of files named
 <tt>refXXXXX.map</tt>, where <tt>XXXXX</tt> is the 0-padded index of the reference
 sequence aligned to.  Useful for dealing with large datasets
 aligned to, e.g., the assembled human genome.
 <li>Improved tutorial to use a simple simulated read set (included)
 to do SNP calls with Maq.</li>
 <li>Added <a href="manual.shtml#bowtie-build-options-ntoa"><tt>--nota</tt></a> option to <tt>bowtie-build</tt></li>
 <li>Fixed <tt>make_h_sapiens_asm.sh</tt> script to include mitochondrial DNA.</li>
  </ul>
  <br/>
<h2>0.9.8 release - 11/25/08</h2>
  <ul>
  <li><tt>--unfa</tt>/<tt>--unfq &lt;filename&gt;</tt> options cause bowtie to dump unaligned
      reads to FASTA and/or FASTQ files.</li>
  <li><tt>bowtie-build</tt> now selects its memory-efficiency parameters (<tt>--bmax</tt>,
 <tt>--dcv</tt>, <tt>--packed</tt>) automatically by default; this makes it far
 easier to build an index under memory constraints by eliminating
 tedious trail-and-error.  New <a href="manual.shtml#bowtie-build-options-a"><tt>-a</tt></a> option disables this, yielding
 old behavior.</li>
  <li><tt>bowtie-build-packed</tt> is no longer a separate binary.  Supplying the
 new <a href="manual.shtml#bowtie-build-options-p"><tt>-p</tt>/<tt>--packed</tt></a> argument to <tt>bowtie-build</tt> is the new equivalent.</li>
  <li>New tool <tt>bowtie-maptool</tt> converts between Bowtie's output formats.</li>
  <li>New tool <a href="manual.shtml#the-bowtie-inspect-index-inspector"><tt>bowtie-inspect</tt></a> recreates reference strings from Bowtie
 index.</li>
  <li>Renamed <tt>bowtie-convert</tt> to <tt>bowtie-maqconvert</tt> for clarity.</li>
  <li>New universal Mac binary combines i386 & x86_64 binaries.  PowerPC
 still not supported.</li>
  <li>Added <a href="manual.shtml#bowtie-options-nomaqround"><tt>--nomaqround</tt></a> option to <tt>bowtie</tt>.</li>
  <li>Fixed memory leaks in <tt>bowtie</tt>.</li>
  <li>Switched to a new scheme for mapping positions in "joined"
 reference string to positions in original strings.  This changes
 the index format.  <tt>bowtie-build</tt>'s <tt>--oldpmap</tt> parameter reverts to
 the old format.  Versions of <tt>bowtie</tt> prior to 0.9.8 cannot search
 indexes produced by <tt>bowtie-build</tt> 0.9.8 unless <tt>bowtie-build</tt> is
 run with <tt>--oldpmap</tt>.  <tt>bowtie</tt> 0.9.8 can search either index format.
 Pre-built indexes are still in the old format, but will switch to
 new format when Bowtie 1.0 is released.</li>
  </ul>
  <br/>

<h2>0.9.7.1 release - 11/11/08</h2>
  <ul>
  <li>Fixed an issue that caused a spurious loss of sensitivity between
 Bowtie versions 0.9.6 and 0.9.7 in certain modes.  Many thanks to
 Ali Mortazavi for bringing this to our attention.</li>
  </ul>
  <br/>

<h2>TopHat released - 11/8/08</h2>
  <ul>
  <li>Cole Trapnell has completed the initial release of
      <a href="http://tophat.cbcb.umd.edu">TopHat</a>, a fast splice junction mapper
      for RNA-Seq reads. TopHat aligns RNA-Seq reads to mammalian-sized genomes using
      Bowtie, and then analyzes the mapping results to identify splice junctions
      between exons. 
  </li>
  </ul>
  <br/>
  <h2>Illumina link - 10/22/08</h2>
  <ul>
  <li>Bowtie is now listed on Illumina's <a href="http://www.illumina.com/pagesnrn.ilmn?ID=245">third-party tools</a> page</li>
  </ul>
  <br/>
  <h2>Coming soon...</h2>
  <ul>
  	<li>A new addition to the Bowtie family: Tophat.  Tophat is a complete
  	Bowtie-based toolchain for RNA-seq applications.  Check back soon for the
  	official release.</li>
  </ul>
  <br/>
  <h2>0.9.6 release - 10/10/08</h2>
  <ul>
  	<li><tt>bowtie</tt> now supports a host of options that allow the user to
    specify which and how many valid alignments to report per read.
    The default is still to report 1 "good" alignment, which is by far
    the fastest mode.  See <a href="manual.shtml#reporting-modes"><tt>-k/-a/--best/--nostrata</tt></a> options described
    in the manual for details.</li>
 	<li><tt>bowtie</tt> now supports reads up to 1024 bases long.  Note that for
    reads much longer than, say, 35 bases, the user must be careful to
    set alignment policy parameters (especially <tt>-e</tt>) appropriately.</li>
 	<li><tt>--fast</tt> flag eliminated, double-index mode is now the default.
    Added the <tt>-z/--phased</tt> flag to revert to phased, half-index mode.</li>
 	<li><tt>--concise</tt> output mode now officially supported.  Now outputs one
    alignment per line.</li>
 	<li>Changed <tt>bowtie-build</tt> default back to <tt>--bmaxdivn 4</tt>.</li>
 	<li><tt>-h/--help</tt> now prints much more verbose help for <tt>bowtie</tt> and
    <tt>bowtie-build</tt> (verbatim from <tt>MANUAL</tt> file).</li>
 	<li>BWT-searching code streamlined; much old code eliminated</li>
  </ul>
  <br/>
  <h2>0.9.5 release - 9/27/08</h2>
  <ul>
      <li>Last column of output now additionally reports the reference and
      query bases (in that order) for mismatches.  E.g., old: <tt>30,32</tt>
      new: <tt>30:C>A,32:C>T</tt>.</li>
      <li>Eliminated spurious trailing space in first column of output.</tt>
      <li>Minor performance and sensitivity improvements.</li>
      <li>New option <tt>-p</tt> spawns a user-specified number of pthreads for
      parallel processing of reads.  For example, use <tt>-p 4</tt> to run
      <tt>bowtie</tt> on 4 processor cores simultaneously.</li>
      <li>Due to the new <tt>-p</tt> option, <tt>bowtie</tt> needs pthreads to compile and run.
      To compile <tt>bowtie</tt> without pthreads support (which disables the
      <tt>-p</tt> option), use <tt>make BOWTIE_PTHREADS=0</tt>.</li>
      <li>Also due to '-p' option, the Windows version of Bowtie now comes with
      the <tt>pthreadGC2.dll</tt> file from the <a href="http://sourceware.org/pthreads-win32">pthreads for Win32 project</a>.
      This library is released under the <a href="http://sourceware.org/pthreads-win32/copying.html">LGPL license</a>.
      <li>New option <tt>--fast</tt> causes Bowtie to load both the "forward" and
      "mirror" halves of the index at once, which eliminates the need
      for multiple phases and speeds up matching at the cost of using
      about twice as much memory.  <tt>--fast</tt> also causes <tt>bowtie</tt> to
      scale better when used in combination with <tt>-p</tt>.</li>
      <li>Fixed crashing bug with <tt>-o/--offrate</tt> in <tt>bowtie</tt>.
      <li>Improved error reporting.</li>
  </ul>
  <br/>
  <h2>0.9.4 release - 9/16/08</h2>
  <ul>
      <li>New method for handling gaps and ambiguity codes in the reference.
      New <tt>bowtie-build</tt> handles long stretches of gaps
      gracefully.  New <tt>bowtie</tt> rejects alignments that overlap a gap or
      ambiguous character in the reference.</li>
      <li>Due to above change, index file format has been changed.  All
      pre-built indexes available on this site have been updated to the
      new format.  To obtain indexes with the old format, contact us.</li>
      <li>In <tt>bowtie</tt> unnamed reads are now given ordinal names (rather than
      "default") in the alignment output.  Works for all input modes.</li>
      <li>New <tt>bowtie</tt> input mode: Raw, activated with <tt>-r</tt>.  Expects one read
      sequence per line; no quality values or names.</li>
      <li>Fixed <tt>bowtie</tt> bug whereby trimming did not work in <tt>-c</tt> mode.</li>
      <li>Changed <tt>bowtie-build</tt> default to not use blockwise mode.</li>
      <li>Fixed <tt>bowtie-build</tt> to avoid certain infinite-loop and
      very-long-runtime scenarios.</li>
      <li>Packaging improvements: archives now explode into subdirectories
      and scripts are executable.</li>
  </ul>
  <br/>
  <h2>0.9.3 release - 9/6/08</h2>
  <ul>
      <li>Major reference-name bug fixes to <tt>bowtie-convert</tt></li>
  </ul>
  <br/>
  <h2>0.9.2 release - 9/4/08</h2>
  <ul>
      <li>Now allows 3-mismatches: <tt>-n</tt> and <tt>-v</tt> options accept 3</li>
      <li>Output format prints reference name instead of id in third column</li>
      <li>Pre-built indexes updated to encode reference names</li>
      <li>Ns in reads now match nothing (previously, they matched As/Ts)</li>
      <li>Dropped <tt>-l/--linerate</tt> and <tt>-i/--linesperside</tt> arguments to <tt>bowtie-build</tt></li>
      <li>Fixed bug in Maq-like mode that allowed some poor alignments</tt>
      <li>Minor speed improvements</li>
  </ul>
  <br/>
  <h2>0.9.1 release - 8/25/08</h2>
  <ul>
      <li>Integrated relevant SeqAn-1.1 sources into Bowtie source release</li>
      <li>Now builds on Windows under <a href="http://www.mingw.org/">MinGW</a> (needs <a href="http://sourceware.org/pthreads-win32/">pthreads</a> and <a href="http://cygwin.com/packages/mingw-zlib/">zlib</a>)</li>
      <li>Binary releases for Linux (i386, x86_64), Windows (i386) and MacOS X (i386)</li>
  </ul>
  <br/>
  <h2>0.9.0 release - 8/18/08</h2>
  <p>The first public release of the Bowtie source is now available for
     download.  The release includes the three core Bowtie tools: the
     indexer <span style="FONT-FAMILY:Courier New">bowtie-build</span>,
     the read aligner <span style="FONT-FAMILY:Courier New">bowtie</span> and
     the converter from Bowtie's to Maq's mapping output format,
     <span style="FONT-FAMILY:Courier New">bowtie-convert</span>.  This is a stable release, and compatible
     pre-built indexes for many model organisms are also available.  See
     "Source releases" and "Pre-built indexes" on the sidebar.  Please
     report any issues using the Sourceforge
     <a href="https://sourceforge.net/tracker/?atid=1101606&group_id=236897&func=browse">bug tracker</a>.</p>
  <p>Features of this release include:
  <ul>
      <li>FASTA, FASTQ inputs supported; tested with Solexa FASTQ</li>
      <li>Supports Maq alignment policy (<tt>-n</tt> and <tt>-e</tt> behave as in Maq)</li>
      <li>Supports X-mismatch policy (<tt>-v</tt> option behaves as in SOAP)</li>
      <li><tt>-n</tt> and <tt>-v</tt> options accept 0, 1, or 2</li>
  </ul>
