AlphaSeqOpt specifications


Unique identifier OMICS_22374
Name AlphaSeqOpt
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format TXT
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.1.1
Stability No
Maintained Yes


No version available


  • person_outline Roger Ros-Freixedes
  • person_outline Serap Gonen
  • person_outline Gregor Gorjanc
  • person_outline John Hickey

Publication for AlphaSeqOpt

AlphaSeqOpt citations


A method for allocating low coverage sequencing resources by targeting haplotypes rather than individuals

PMCID: 5655873
PMID: 29070022
DOI: 10.1186/s12711-017-0353-y
call_split See protocol

[…] e function. In the second step, referred to as ‘set refinement’, the initial set of individuals is refined through several rounds of exchanges. The method was implemented in a software package called AlphaSeqOpt, which also implements the method of Gonen et al. []. Throughout the rest of the paper, AlphaSeqOpt is used when referring to our method. […]


A method for the allocation of sequencing resources in genotyped livestock populations

PMCID: 5437657
PMID: 28521728
DOI: 10.1186/s12711-017-0322-5
call_split See protocol

[…] resent the maximum possible portion of the haplotype diversity in the population that can be sequenced and phased for a fixed sequencing budget. We implemented our method in a software package called AlphaSeqOpt. Throughout the rest of the paper, AlphaSeqOpt is used when referring to our method. An outline of each algorithm is given below. […]

AlphaSeqOpt institution(s)
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, UK
AlphaSeqOpt funding source(s)
Supported by the BBSRC ISPG to The Roslin Institute BB/J004235/1, by Genus PLC and by grant numbers BB/M009254/1, BB/L020726/1, BB/N004736/1, BB/N004728/1, BB/L020467/1, BB/N006178/1, Medical Research Council (MRC) grant number MR/M000370/1 and the Edinburgh Compute and Data Facility (ECDF).

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