Automated simultaneous analysis phylogenetics (ASAP): An enabling tool for phlyogenomics

Indra Neil Sarkar; Mary G. Egan; Gloria Coruzzi; Ernest K. Lee; Rob DeSalle

doi:10.1186/1471-2105-9-103

Automated simultaneous analysis phylogenetics (ASAP): An enabling tool for phlyogenomics

Indra Neil Sarkar, Mary G. Egan, Gloria Coruzzi, Ernest K. Lee, Rob DeSalle

Biology and Genomics

Research output: Contribution to journal › Article › peer-review

Abstract

Background: The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices. Results: To keep pace with the exponentially growing volume of molecular data in the genomic era, we have developed an automated technique, ASAP (Automated Simultaneous Analysis Phylogenetics), to assemble these multigene/multi species matrices and to evaluate the significance of individual genes within the context of a given phylogenetic hypothesis. Conclusion: Applications of ASAP may enable scientists to re-evaluate species relationships and to develop new phylogenomic hypotheses based on genome-scale data.

Original language	English (US)
Article number	103
Journal	BMC bioinformatics
Volume	9
DOIs	https://doi.org/10.1186/1471-2105-9-103
State	Published - Feb 19 2008

ASJC Scopus subject areas

Structural Biology
Biochemistry
Molecular Biology
Computer Science Applications
Applied Mathematics

Access to Document

10.1186/1471-2105-9-103

Cite this

@article{32a5d25db57f47aea0ff967f6e6db825,

title = "Automated simultaneous analysis phylogenetics (ASAP): An enabling tool for phlyogenomics",

abstract = "Background: The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices. Results: To keep pace with the exponentially growing volume of molecular data in the genomic era, we have developed an automated technique, ASAP (Automated Simultaneous Analysis Phylogenetics), to assemble these multigene/multi species matrices and to evaluate the significance of individual genes within the context of a given phylogenetic hypothesis. Conclusion: Applications of ASAP may enable scientists to re-evaluate species relationships and to develop new phylogenomic hypotheses based on genome-scale data.",

author = "Sarkar, {Indra Neil} and Egan, {Mary G.} and Gloria Coruzzi and Lee, {Ernest K.} and Rob DeSalle",

note = "Funding Information: The authors wish to thank E. Brenner, E.K. Lienau, E. de LaTorre, P.J. Planet, and members of the New York Plant Genomics Consortium. This work is funded in part by NSF DBI-0421604 to GC and RD. INS is supported in part by the Ellison Medical Foundation.",

year = "2008",

month = feb,

day = "19",

doi = "10.1186/1471-2105-9-103",

language = "English (US)",

volume = "9",

journal = "BMC bioinformatics",

issn = "1471-2105",

publisher = "BioMed Central",

}

TY - JOUR

T1 - Automated simultaneous analysis phylogenetics (ASAP)

T2 - An enabling tool for phlyogenomics

AU - Sarkar, Indra Neil

AU - Egan, Mary G.

AU - Coruzzi, Gloria

AU - Lee, Ernest K.

AU - DeSalle, Rob

N1 - Funding Information: The authors wish to thank E. Brenner, E.K. Lienau, E. de LaTorre, P.J. Planet, and members of the New York Plant Genomics Consortium. This work is funded in part by NSF DBI-0421604 to GC and RD. INS is supported in part by the Ellison Medical Foundation.

PY - 2008/2/19

Y1 - 2008/2/19

N2 - Background: The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices. Results: To keep pace with the exponentially growing volume of molecular data in the genomic era, we have developed an automated technique, ASAP (Automated Simultaneous Analysis Phylogenetics), to assemble these multigene/multi species matrices and to evaluate the significance of individual genes within the context of a given phylogenetic hypothesis. Conclusion: Applications of ASAP may enable scientists to re-evaluate species relationships and to develop new phylogenomic hypotheses based on genome-scale data.

AB - Background: The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices. Results: To keep pace with the exponentially growing volume of molecular data in the genomic era, we have developed an automated technique, ASAP (Automated Simultaneous Analysis Phylogenetics), to assemble these multigene/multi species matrices and to evaluate the significance of individual genes within the context of a given phylogenetic hypothesis. Conclusion: Applications of ASAP may enable scientists to re-evaluate species relationships and to develop new phylogenomic hypotheses based on genome-scale data.

UR - http://www.scopus.com/inward/record.url?scp=41049110434&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=41049110434&partnerID=8YFLogxK

U2 - 10.1186/1471-2105-9-103

DO - 10.1186/1471-2105-9-103

M3 - Article

C2 - 18282301

AN - SCOPUS:41049110434

SN - 1471-2105

VL - 9

JO - BMC bioinformatics

JF - BMC bioinformatics

M1 - 103

ER -

Automated simultaneous analysis phylogenetics (ASAP): An enabling tool for phlyogenomics

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this