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


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Maintainer


  • person_outline Jian Ma <>

Publication for inferCars

inferCars in publications

 (5)
PMCID: 5635614
PMID: 29081686
DOI: 10.2174/1389202918666170307120943

[…] and genome regions into ancestral genomes along the internal node of the given phylogeny. homology/adjacency-based approaches are explored more frequently in recent years, such as pmag [], infercars [], procars [], anges [] and gapped adjacency []., distance/event-based approaches are computationally costly and time-consuming since they usually need to solve the problems of np-hard […]

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

[…] 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, […]

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 […]

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

[…] (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 […]

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

[…] 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, […]


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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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