Using installed software (modules)

- Package -----------------------------+- Versions -+- Last mod. ------
/opt/compsci/modulefiles:
454/default                                          2016/07/07 13:39:48
abacas/1.03                                          2016/04/05 15:01:20
abyss/1.9.0                                          2016/04/05 15:04:06
abyss/1.9.0-mpi                                      2016/07/28 15:00:24
act/13.0.0                                           2015/03/30 16:23:58
aga/0.1.0                                default     2016/08/24 16:24:17
aga/latest                                           2016/08/24 16:12:16
aga/test                                             2016/08/24 16:06:09
alamut/1.5.2                                         2016/09/14 16:14:14
alamut/1.5.2-standalone                              2016/10/14 18:15:59
alamut/1.5.2-test                                    2016/10/10 19:12:20
allpaths/52488                                       2016/04/18 13:35:44
amos/3.1.0                                           2015/11/25 15:03:53
Anaconda/2.4.0                                       2015/11/12 16:32:09
annovar/2014-11-12                                   2015/03/24 12:06:45
annovar/2015-03-22                                   2015/03/24 12:17:45
ant/1.9.4                                            2014/09/12 20:31:54
antismash/3.0                                        2016/08/05 13:51:40
apt/1.15.0                                           2015/08/12 19:00:15
armadillo/4.100.2                                    2014/04/01 15:35:07
artemis/13.0.0                                       2015/03/30 16:23:58
aspera/default                                       2015/12/23 13:04:29
BACH/070913                                          2014/04/01 22:22:29
bam-readcount/0                                      2014/11/28 17:14:08
bamtools/1.0.2                           default     2014/04/28 16:18:54
bamtools/2.3.0                                       2014/05/15 15:54:18
baysic/default                                       2015/10/19 15:28:00
bbmap/33.73                                          2014/11/06 18:01:45
bbmap/36.14                                          2016/07/07 19:10:59
...                                                  ...
ViennaRNA/2.1.7                                      2014/05/27 17:46:30
vim/7.4                                              2014/03/03 19:15:22
vim/7.4.1640                                         2016/03/23 20:25:40
vim/8.0                                              2016/12/05 22:46:01
WASP/default                                         2015/12/23 19:41:04
weblogo/2.8.2                                        2016/10/12 21:43:38
wgs/8.1                                              2014/03/04 13:28:11
wgs/8.3rc2                                           2015/06/25 17:03:54
xenome/1.0.0                                         2012/09/26 18:55:37
xlwt/0.7.4                                           2013/02/15 18:26:18
zsh/5.0.5                                            2014/03/03 19:32:18

Bowtie 2 version 2.2.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage:
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]

  <bt2-idx>  Index filename prefix (minus trailing .X.bt2).
             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <sam>      File for SAM output (default: stdout)

  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

 Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
  --qseq             query input files are in Illumina's qseq format
  -f                 query input files are (multi-)FASTA .fa/.mfa
  -r                 query input files are raw one-sequence-per-line
  -c                 <m1>, <m2>, <r> are sequences themselves, not files
  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)
  -u/--upto <int>    stop after first <int> reads/pairs (no limit)
  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)
  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)
  --phred33          qualities are Phred+33 (default)
  --phred64          qualities are Phred+64
  --int-quals        qualities encoded as space-delimited integers

 Presets:                 Same as:
  For --end-to-end:
   --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
   --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
   --sensitive            -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
   --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

  For --local:
   --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
   --fast-local           -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
   --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
   --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

 Alignment:
  -N <int>           max # mismatches in seed alignment; can be 0 or 1 (0)
  -L <int>           length of seed substrings; must be >3, <32 (22)
  -i <func>          interval between seed substrings w/r/t read len (S,1,1.15)
  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
  --dpad <int>       include <int> extra ref chars on sides of DP table (15)
  --gbar <int>       disallow gaps within <int> nucs of read extremes (4)
  --ignore-quals     treat all quality values as 30 on Phred scale (off)
  --nofw             do not align forward (original) version of read (off)
  --norc             do not align reverse-complement version of read (off)
  --no-1mm-upfront   do not allow 1 mismatch alignments before attempting to
                     scan for the optimal seeded alignments
  --end-to-end       entire read must align; no clipping (on)
   OR
  --local            local alignment; ends might be soft clipped (off)

 Scoring:
  --ma <int>         match bonus (0 for --end-to-end, 2 for --local)
  --mp <int>         max penalty for mismatch; lower qual = lower penalty (6)
  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)
  --rdg <int>,<int>  read gap open, extend penalties (5,3)
  --rfg <int>,<int>  reference gap open, extend penalties (5,3)
  --score-min <func> min acceptable alignment score w/r/t read length
                     (G,20,8 for local, L,-0.6,-0.6 for end-to-end)

 Reporting:
  (default)          look for multiple alignments, report best, with MAPQ
   OR
  -k <int>           report up to <int> alns per read; MAPQ not meaningful
   OR
  -a/--all           report all alignments; very slow, MAPQ not meaningful

 Effort:
  -D <int>           give up extending after <int> failed extends in a row (15)
  -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)

 Paired-end:
  -I/--minins <int>  minimum fragment length (0)
  -X/--maxins <int>  maximum fragment length (500)
  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
  --no-mixed         suppress unpaired alignments for paired reads
  --no-discordant    suppress discordant alignments for paired reads
  --no-dovetail      not concordant when mates extend past each other
  --no-contain       not concordant when one mate alignment contains other
  --no-overlap       not concordant when mates overlap at all

 Output:
  -t/--time          print wall-clock time taken by search phases
  --un <path>           write unpaired reads that didn't align to <path>
  --al <path>           write unpaired reads that aligned at least once to <path>
  --un-conc <path>      write pairs that didn't align concordantly to <path>
  --al-conc <path>      write pairs that aligned concordantly at least once to <path>
  (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
  --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
  --quiet            print nothing to stderr except serious errors
  --met-file <path>  send metrics to file at <path> (off)
  --met-stderr       send metrics to stderr (off)
  --met <int>        report internal counters & metrics every <int> secs (1)
  --no-head          supppress header lines, i.e. lines starting with @
  --no-sq            supppress @SQ header lines
  --rg-id <text>     set read group id, reflected in @RG line and RG:Z: opt field
  --rg <text>        add <text> ("lab:value") to @RG line of SAM header.
                     Note: @RG line only printed when --rg-id is set.
  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments.

 Performance:
  -p/--threads <int> number of alignment threads to launch (1)
  --reorder          force SAM output order to match order of input reads
  --mm               use memory-mapped I/O for index; many 'bowtie's can share

 Other:
  --qc-filter        filter out reads that are bad according to QSEQ filter
  --seed <int>       seed for random number generator (0)
  --non-deterministic seed rand. gen. arbitrarily instead of using read attributes
  --version          print version information and quit
  -h/--help          print this usage message

Currently Loaded Modulefiles:
1) bowtie2/2.2.3

Currently Loaded Modulefiles:
  1) bowtie2/2.2.3

No Modulefiles Currently Loaded.

 **************************************************************
 ******** CLUSTAL 2.1 Multiple Sequence Alignments  ********
 **************************************************************


     1. Sequence Input From Disc
     2. Multiple Alignments
     3. Profile / Structure Alignments
     4. Phylogenetic trees

     S. Execute a system command
     H. HELP
     X. EXIT (leave program)


Your choice: H
Clustal W is a general purpose multiple alignment program for DNA or proteins.

SEQUENCE INPUT:  all sequences must be in 1 file, one after another.
7 formats are automatically recognised: NBRF-PIR, EMBL-SWISSPROT,
Pearson (Fasta), Clustal (\*.aln), GCG-MSF (Pileup), GCG9-RSF and GDE flat file.
All non-alphabetic characters (spaces, digits, punctuation marks) are ignored
except "-" which is used to indicate a GAP ("." in MSF-RSF).

To do a MULTIPLE ALIGNMENT on a set of sequences, use item 1 from this menu to
INPUT them; go to menu item 2 to do the multiple alignment.

PROFILE ALIGNMENTS (menu item 3) are used to align 2 alignments.  Use this to
add a new sequence to an old alignment, or to use secondary structure to guide
the alignment process.  GAPS in the old alignments are indicated using the "-"
character.   PROFILES can be input in ANY of the allowed formats; just
use "-" (or "." for MSF-RSF) for each gap position.

PHYLOGENETIC TREES (menu item 4) can be calculated from old alignments (read in
with "-" characters to indicate gaps) OR after a multiple alignment while the
alignment is still in memory.


Press [RETURN] to continue or  X  to stop