Read & reformat biosequences, Java command-line version
  Usage: jre -cp readseq.jar run [options] input-file(s)

  Options
    -a[ll]              select All sequences
    -c[aselower]        change to lower case
    -C[ASEUPPER]        change to UPPER CASE
    -degap[=-]          remove gap symbols
    -i[tem=2,3,4]       select Item number(s) from several
    -l[ist]             List sequences only
    -o[utput=]out.seq   redirect Output
    -p[ipe]             Pipe (command line, stdout)
    -t[ranslate=]io     translate input symbol [i] to output symbol [o]
                        use several -tio to translate several symbols
    -v[erbose]          Verbose progress
    -f[ormat=]#         Format number for output,  or
    -f[ormat=]Name      Format name for output
          see Formats   list below for names and numbers
    -inform[at]=#       input format number,  or
    -inform[at]=Name    input format name.  Assume input data is this format
    -ch[ecksum]         calculate & print checksum of sequences

   Document field and Feature table extraction:
    -feat[ures]=exon,CDS...   extract sequence of selected features
    -nofeat[ures]=repeat_region,intron... remove sequence of selected features 
    -field=AC,ID...      include selected document fields in output
    -nofield=COMMENT,... remove selected document fields from output 

   Pretty format options:
    -wid[th]=#            sequence line width
    -tab=#                left indent
    -col[space]=#         column space within sequence line on output
    -gap[count]           count gap chars in sequence numbers
    -nameleft, -nameright[=#]   name on left/right side [=max width]
    -nametop              name at top/bottom
    -numleft, -numright   seq index on left/right side
    -numtop, -numbot      index on top/bottom
    -match[=.]            use match base for 2..n species
    -inter[line=#]        blank line(s) between sequence blocks

This program requires a Java runtime (jre) program, version 1.1.x 
The leading '-' on option is optional if '=' is present.  All non-options
(no leading '-' or embedded '=') are used as input file names.
These options and call format are compatible with the classic readseq (v.1992)
with exception of no -reverse option.


Readseq version 2.0.10 (27 May 2000)

Home of this package is http://iubio.bio.indiana.edu/soft/molbio/readseq/java/

An instance of the Web form for this is http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi

For further information on feature tables, see http://www.ncbi.nlm.nih.gov/collab/FT/index.html


Known biosequence formats:
IDNameReadWriteInt'leafDocumentContent-typeSuffix
1IG|Stanfordyes yes -- -- biosequence/ig.ig
2GenBank|GByes yes -- yes biosequence/genbank.gb
3NBRFyes yes -- -- biosequence/nbrf.nbrf
4EMBLyes yes -- yes biosequence/embl.embl
5GCGyes yes -- -- biosequence/gcg.gcg
6DNAStrideryes yes -- -- biosequence/strider.strider
7Fitch-- -- -- -- biosequence/fitch.fitch
8Pearson|Fastayes yes -- -- biosequence/fasta.fasta
9Zuker-- -- -- -- biosequence/zuker.zuker
10Olsen-- -- yes -- biosequence/olsen.olsen
11Phylip3.2yes yes yes -- biosequence/phylip2.phylip2
12Phylip|Phylip4yes yes yes -- biosequence/phylip.phylip
13Plain|Rawyes yes -- -- biosequence/plain.seq
14PIR|CODATAyes yes -- -- biosequence/codata.pir
15MSFyes yes yes -- biosequence/msf.msf
16PAUP|NEXUSyes yes yes -- biosequence/nexus.nexus
17Pretty-- yes yes -- biosequence/pretty.pretty
18XMLyes yes -- yes biosequence/xml.xml
19BLASTyes -- yes -- biosequence/blast.blast
20SCFyes -- -- -- biosequence/scf.scf
21ASN.1-- -- -- -- biosequence/asn1.asn
   (Int'leaf = interleaved format; Document = documentation is parsed)

Also available in this package:

For the current help document, use
jre -cp readseq.jar help


  Graphic interface to Readseq (Java swing)
  Usage:
    java -cp readseq.jar iubio.readseq.app (java version 1.2)
    jre -cp readseq.jar:/path/to/swingall.jar iubio.readseq.app (java version 1.1.x)
  Readseq version 2.0.10 (27 May 2000)

  Java Foundation Classes (Swing) are required for this interface
  This is available for Java versions 1.1.7 and newer at
     http://java.sun.com/products/jfc/download.html
  Put the swingall.jar of this package in your classpath, as with
    jre -cp readseq.jar:swingall.jar iubio.readseq.app (java version 1.1.x)

  Macintosh users: See also Readseq.macapp, a small Mac Java application
  to launch readseq.jar without a jre commandline.


HTTP server common gateway interface to Readseq Usage (example as cgi on unix system): Install shell script like this as '/cgi-bin/readseq.cgi' for your web server #!/bin/sh envtemp=/tmp/rseq$$.env env > ${envtemp} /usr/java/bin/jre -cp readseq.jar iubio.readseq.cgi env=${envtemp} /bin/rm ${envtemp} Readseq version 2.0.10 (27 May 2000) See also iubio.readseq.run.usage()