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GapAdj specifications

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Unique identifier OMICS_12585
Name GapAdj
Alternative name Gapped Adjacencies
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A set of modern genomes, a species tree S with leaves labeled with genomes, and an internal node of representing a speciation event of interest
Output data An ancestral genome at node ν
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Dia El-Mabrouk <>

Publication for Gapped Adjacencies

GapAdj citations

 (4)
library_books

Ancestral Genome Reconstruction on Whole Genome Level

2017
PMCID: 5635614
PMID: 29081686
DOI: 10.2174/1389202918666170307120943

[…] and losses and duplication []. gapped adjacency introduced a cutoff threshold t and constant value maxa among contiguous ancestral regions, and reconnected the neighboring regions by considering gapped adjacencies. this algorithm iterated in a two-step procedure, which determined the genome content and multiplicity for each ancestral node in the first step. it increased the value from 1 […]

library_books

Fast ancestral gene order reconstruction of genomes with unequal gene content

2016
PMCID: 5123410
PMID: 28185578
DOI: 10.1186/s12859-016-1261-9

[…] function that might combine factors such as maximization of weights or probabilities, and minimizing character changes in the tree. notable examples include the pioneer infercars [], as well as gapadj [], anges [], pmag + [, ], procars [] and physca []., in our recent contribution to this field, we proposed a method that combines ideas from homology-based methods, namely adjacency weights, […]

library_books

Reconstruction of ancestral gene orders using intermediate genomes

2015
PMCID: 4602182
PMID: 26451811
DOI: 10.1186/1471-2105-16-S14-S3

[…] or gene clusters, and use this information to assemble contiguous ancestral regions (cars), as pioneered by ma et al. in infercars [], an approach explored by many recent algorithms, such as gapadj [], anges [], pmag [], mlgo [] and procars []., in this paper, a new approach is proposed, inspired by combinatorial ideas from rearrangement models, though not directly motivated […]

library_books

Reconstruction of Ancestral Gene Orders Using Probabilistic and Gene Encoding Approaches

2014
PMCID: 4193752
PMID: 25302942
DOI: 10.1371/journal.pone.0108796

[…] while more recent methods based on gene adjacencies such as infercarspro is relatively faster, but often produces an excessive number of chromosomes. this issue is mitigated by newer methods such as gapadj, however it sacrifices a considerable portion of accuracy. we recently developed an adjacency-based method in the probabilistic framework called pmag to infer ancestral gene orders. pmag […]


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GapAdj institution(s)
Département d’Informatique (DIRO), Université de Montréal, Montréal, Canada; McGill Centre for Bioinformatics, McGill University, Montréal, Canada

GapAdj review

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zakari

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hello everyone, I am new in the community and I want to make an analysis that compares three PROCARS, GapAdj and Intercars, so I ask your help if you please