LAGAN specifications

Information


Unique identifier OMICS_08469
Name LAGAN
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Serafim Batzoglou <>

Information


Unique identifier OMICS_08469
Name LAGAN
Software type Application/Script, Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Source code URL http://lagan.stanford.edu/lagan_web/lagan20.tar.gz
Maintained Yes

Versioning


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Maintainer


  • person_outline Serafim Batzoglou <>

LAGAN articles

LAGAN citations

 (4)
2015
PMCID: 4551851

[…] nov 2009), coelacanth (latcha1, insdc assembly, sep 2011), medaka (hdrr, oct 2005) and spotted gar (lepocu1, insdc assembly, dec 2011). global pairwise alignment was carried out using shuffle-lagan [32], and the results were visualized using the vista browser [33]. conserved transcription factor binding consensus sequences were identified using rvista [34] and visual inspection […]

2015
PMCID: 4470032

[…] and protein sequences were analyzed., phylogenetic trees were constructed using hox cluster sequences and the 623 orthologous genes. the four hox clusters from various gnathostomes were aligned with lagan. and the 623 orthologous genes were aligned with muscle 3.6. the ambiguous positions in each alignment were eliminated by gblocks (version 0.91b) with half gaps allowed. maximum likelihood […]

2010
PMCID: 3185746

[…] one large contiguous alignment for subsequent phylogenetic analysis. for the core orthopoxvirus genome nucleotide alignment, the alignment was generated using a combination of the programs mavid and multi-lagan [93,94]. the final computational alignment was then hand edited extensively to optimize the alignment. the alignment extends from base 15716 to base 158673 of the vaccinia virus strain […]

2010
PMCID: 2885371

[…] system but which used a blackboard for communication, rather than a distributed object communication method., over time, we will want to change some parts of our pipeline. for instance, multi-lagan [20] was used in our pipelines to build multiple alignments before the deployment of pecan [14]. similarly, our most current analysis pipeline uses enredo [14] rather than mercator [12], […]

LAGAN institution(s)
Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Pathology and Department of Genetics, Stanford University, Stanford, CA, USA; Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
LAGAN funding source(s)
Supported by an NSF Graduate Fellowship; a Howard Hughes Medical Institute predoctoral fellowship; and funds from the National Human Genome Research Institute.

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