mira-assembler 4.0.2-1 (amd64 binary) in ubuntu wily

 The mira genome fragment assembler is a specialised assembler for
 sequencing projects classified as 'hard' due to high number of similar
 repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
 specialised on reconstructing pristine mRNA transcripts while
 detecting and classifying single nucleotide polymorphisms (SNP)
 occuring in different variations thereof.
 .
 The assembler is routinely used for such various tasks as mutation
 detection in different cell types, similarity analysis of transcripts
 between organisms, and pristine assembly of sequences from various
 sources for oligo design in clinical microarray experiments.
 .
 The package provides the following executables:
 Binaries provided:
  * mira: for assembly of genome sequences
  * miramem: estimating memory needed to assemble projects. Realised through
    link to mira.
  * convert_project: for converting project file types into other types
  * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
    frequently used file converters (realised through links to convert_project)
  * scftool: set of tools useful when working with SCF trace files
  * fastatool: set of tools useful when working with FASTA trace files
 .
 Scripts provided:
  * fasta2frag: fragmenting sequences into smaller, overlapping
    subsequences. Useful for simulating shotgun sequences. Can create
    subsequences in both directions (/default) and also paired-end sequences.
  * fastaselect: given a FASTA file (and possibly a FASTA quality file) and
    a file with names of reads, select the sequences from the input FASTA (and
    quality file) and writes them to an output FASTA
  * fastqselect: like fastaselect, only for FASTQ
  * fixACE4consed: Consed has a bug which incapacitates it from reading
    consensus tags in ACE files written by the MIRA assembler (and possibly
    other programs). This script massages an ACE file so that consed can read
    the consensus tags.