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Number of citations per year for the bioinformatics software tool inferCars
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Protocols

inferCars specifications

Information


Unique identifier OMICS_12584
Name inferCars
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data The orthology blocks, conserved segments, contiguous ancestral regions, a file that describes which species support each ancestral join, and our list of micro-inversions.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Jian Ma

Publication for inferCars

inferCars citations

 (6)
library_books

Ancestral Genome Reconstruction on Whole Genome Level

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

[…] InferCARs was a Fitch parsimony-based computational heuristic algorithm that predicted the permutations and orientations of conserved segments and orthologous blocks []. This algorithm output the ance […]

library_books

Fast ancestral gene order reconstruction of genomes with unequal gene content

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

[…] und by optimizing an objective 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, name […]

library_books

Reconstruction of ancestral gene orders using intermediate genomes

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

[…] conserved structures between the input genomes, such as conserved adjacencies 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 fr […]

library_books

Comparative genomics reveals birth and death of fragile regions in mammalian evolution

2010
Genome Biol
PMCID: 3156956
PMID: 21118492
DOI: 10.1186/gb-2010-11-11-r117

[…] euse (that requires reconstruction of ancestral genomes) may be affected by errors in reconstruction of ancestral genomes. While various tools for ancestral genome reconstruction (such as MGRA [] and inferCARs []) were shown to be quite accurate (in particular, they produce nearly identical results while using very different algorithms), it is a challenging open problem to evaluate the multispecie […]

library_books

Comparative Analysis of DNA Replication Timing Reveals Conserved Large Scale Chromosomal Architecture

2010
PLoS Genet
PMCID: 2895651
PMID: 20617169
DOI: 10.1371/journal.pgen.1001011

[…] ents we can expect low ToR divergence even around rearrangements, but if the chromosomal neighborhood is a major factor in ToR regulation we would expect significant ToR divergence there. We used the inferCARs algorithm to extract a collection of 1382 syntenic blocks (>50Kb) shared by human, rhesus, mouse, rat and dog, which cover over 92% of the human genome. Using dog as an outgroup, we identif […]

call_split

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes

2010
Bioinformatics
PMCID: 2853686
PMID: 20185404
DOI: 10.1093/bioinformatics/btq079
call_split See protocol

[…] are observed as extant neighbours. We performed extensive simulations and benchmarked our methods against several alternative methods: MGR (Bourque and Pevzner, ), MGRA (Alekseyev and Pevzner, ) and InferCars (Ma et al., ). Our method is the only approach able to satisfactorily analyse data with the volume (53 species and 888 217 extant genes) and complexity (duplications, deletions) found in the […]


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inferCars institution(s)
Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA, USA; Department of Mathematics, National University of Singapore, Singapore; Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA, USA; School of Computer Science, McGill University, Montreal, QC, Canada

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