Staden Package

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Staden Package
Software Details:
Version: 1.7.0 / 2.0.0 Beta 8
Upload Date: 12 May 15
Distribution Type: Freeware
Downloads: 8

Rating: 2.0/5 (Total Votes: 1)

Staden Package is a fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

On the Gap4 front there have been several minor joining related
improvements in how it scores joins in Find Internal Joins and the
functionality of the align button in the Join Editor.

Also of consequence to gap4 are the various changes to io_lib (the
library for all I/O to various trace file formats). With the addition
of a new hash_exp program it now allows for experiment files to be
concatenated together and indexed. The list of experiment file names
should stil be supplied to gap4, but provided the EXP_PATH environment
variable has been set correctly gap4 will be able to fetch individual
sequences out of the concatenated experiment file
archive. Improvements to the user interface for this still need to be
made.

454 SFF archives are now better supported. The defsult 454 indices
now work, although the hash_sff program can be used to provide an
alternative indexing strategy (possibly faster in some cases).

Gap4 and trev also have another trace display style for traces that
have 1 sample scan (x4 channels) per base call. In this case it can
also draw 4 confidence values instead of 1 per base. These abilities
will allow better integration of Solexa traces when more readily
available.

Plus of course the usual mix of bug fixes and minor tweaks. See the
full change log for details (via the SourceForge site).

Other notable changes

Gap4

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