IDEA: Interactive Display for Evolutionary Analyses

<p<Abstract</p< <p<Background</p< <p<The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingl...
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Autor*in:	Carlton Jane M [verfasserIn] Badger Jonathan H [verfasserIn] Crabtree Jonathan [verfasserIn] Mahurkar Anup [verfasserIn] Egan Amy [verfasserIn] Silva Joana C [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2008

Übergeordnetes Werk:	In: BMC Bioinformatics - BMC, 2003, 9(2008), 1, p 524
Übergeordnetes Werk:	volume:9 ; year:2008 ; number:1, p 524

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/1471-2105-9-524

Katalog-ID:	DOAJ064860795

Internformat


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520			\|a <p<Abstract</p< <p<Background</p< <p<The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are <it<codeml </it<and <it<baseml</it<, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.</p< <p<Results</p< <p<We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with <it<codeml </it<and <it<baseml </it<for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.</p< <p<Conclusion</p< <p<IDEA provides a graphical user interface that allows the user to follow a <it<codeml </it<or <it<baseml </it<analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.</p<
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author_variant	c j m cjm b j h bjh c j cj m a ma e a ea s j c sjc
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publishDate	2008
allfields	10.1186/1471-2105-9-524 doi (DE-627)DOAJ064860795 (DE-599)DOAJfee0c8ac514f40148d89f74af69cc530 DE-627 ger DE-627 rakwb eng R858-859.7 QH301-705.5 Carlton Jane M verfasserin aut IDEA: Interactive Display for Evolutionary Analyses 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are <it<codeml </it<and <it<baseml</it<, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.</p< <p<Results</p< <p<We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with <it<codeml </it<and <it<baseml </it<for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.</p< <p<Conclusion</p< <p<IDEA provides a graphical user interface that allows the user to follow a <it<codeml </it<or <it<baseml </it<analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.</p< Computer applications to medicine. Medical informatics Biology (General) Badger Jonathan H verfasserin aut Crabtree Jonathan verfasserin aut Mahurkar Anup verfasserin aut Egan Amy verfasserin aut Silva Joana C verfasserin aut In BMC Bioinformatics BMC, 2003 9(2008), 1, p 524 (DE-627)326644814 (DE-600)2041484-5 14712105 nnns volume:9 year:2008 number:1, p 524 https://doi.org/10.1186/1471-2105-9-524 kostenfrei https://doaj.org/article/fee0c8ac514f40148d89f74af69cc530 kostenfrei http://www.biomedcentral.com/1471-2105/9/524 kostenfrei https://doaj.org/toc/1471-2105 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 1, p 524
spelling	10.1186/1471-2105-9-524 doi (DE-627)DOAJ064860795 (DE-599)DOAJfee0c8ac514f40148d89f74af69cc530 DE-627 ger DE-627 rakwb eng R858-859.7 QH301-705.5 Carlton Jane M verfasserin aut IDEA: Interactive Display for Evolutionary Analyses 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are <it<codeml </it<and <it<baseml</it<, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.</p< <p<Results</p< <p<We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with <it<codeml </it<and <it<baseml </it<for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.</p< <p<Conclusion</p< <p<IDEA provides a graphical user interface that allows the user to follow a <it<codeml </it<or <it<baseml </it<analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.</p< Computer applications to medicine. Medical informatics Biology (General) Badger Jonathan H verfasserin aut Crabtree Jonathan verfasserin aut Mahurkar Anup verfasserin aut Egan Amy verfasserin aut Silva Joana C verfasserin aut In BMC Bioinformatics BMC, 2003 9(2008), 1, p 524 (DE-627)326644814 (DE-600)2041484-5 14712105 nnns volume:9 year:2008 number:1, p 524 https://doi.org/10.1186/1471-2105-9-524 kostenfrei https://doaj.org/article/fee0c8ac514f40148d89f74af69cc530 kostenfrei http://www.biomedcentral.com/1471-2105/9/524 kostenfrei https://doaj.org/toc/1471-2105 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 1, p 524
allfields_unstemmed	10.1186/1471-2105-9-524 doi (DE-627)DOAJ064860795 (DE-599)DOAJfee0c8ac514f40148d89f74af69cc530 DE-627 ger DE-627 rakwb eng R858-859.7 QH301-705.5 Carlton Jane M verfasserin aut IDEA: Interactive Display for Evolutionary Analyses 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are <it<codeml </it<and <it<baseml</it<, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.</p< <p<Results</p< <p<We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with <it<codeml </it<and <it<baseml </it<for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.</p< <p<Conclusion</p< <p<IDEA provides a graphical user interface that allows the user to follow a <it<codeml </it<or <it<baseml </it<analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.</p< Computer applications to medicine. Medical informatics Biology (General) Badger Jonathan H verfasserin aut Crabtree Jonathan verfasserin aut Mahurkar Anup verfasserin aut Egan Amy verfasserin aut Silva Joana C verfasserin aut In BMC Bioinformatics BMC, 2003 9(2008), 1, p 524 (DE-627)326644814 (DE-600)2041484-5 14712105 nnns volume:9 year:2008 number:1, p 524 https://doi.org/10.1186/1471-2105-9-524 kostenfrei https://doaj.org/article/fee0c8ac514f40148d89f74af69cc530 kostenfrei http://www.biomedcentral.com/1471-2105/9/524 kostenfrei https://doaj.org/toc/1471-2105 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 1, p 524
allfieldsGer	10.1186/1471-2105-9-524 doi (DE-627)DOAJ064860795 (DE-599)DOAJfee0c8ac514f40148d89f74af69cc530 DE-627 ger DE-627 rakwb eng R858-859.7 QH301-705.5 Carlton Jane M verfasserin aut IDEA: Interactive Display for Evolutionary Analyses 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are <it<codeml </it<and <it<baseml</it<, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.</p< <p<Results</p< <p<We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with <it<codeml </it<and <it<baseml </it<for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.</p< <p<Conclusion</p< <p<IDEA provides a graphical user interface that allows the user to follow a <it<codeml </it<or <it<baseml </it<analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.</p< Computer applications to medicine. Medical informatics Biology (General) Badger Jonathan H verfasserin aut Crabtree Jonathan verfasserin aut Mahurkar Anup verfasserin aut Egan Amy verfasserin aut Silva Joana C verfasserin aut In BMC Bioinformatics BMC, 2003 9(2008), 1, p 524 (DE-627)326644814 (DE-600)2041484-5 14712105 nnns volume:9 year:2008 number:1, p 524 https://doi.org/10.1186/1471-2105-9-524 kostenfrei https://doaj.org/article/fee0c8ac514f40148d89f74af69cc530 kostenfrei http://www.biomedcentral.com/1471-2105/9/524 kostenfrei https://doaj.org/toc/1471-2105 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 1, p 524
allfieldsSound	10.1186/1471-2105-9-524 doi (DE-627)DOAJ064860795 (DE-599)DOAJfee0c8ac514f40148d89f74af69cc530 DE-627 ger DE-627 rakwb eng R858-859.7 QH301-705.5 Carlton Jane M verfasserin aut IDEA: Interactive Display for Evolutionary Analyses 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are <it<codeml </it<and <it<baseml</it<, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.</p< <p<Results</p< <p<We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with <it<codeml </it<and <it<baseml </it<for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.</p< <p<Conclusion</p< <p<IDEA provides a graphical user interface that allows the user to follow a <it<codeml </it<or <it<baseml </it<analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.</p< Computer applications to medicine. Medical informatics Biology (General) Badger Jonathan H verfasserin aut Crabtree Jonathan verfasserin aut Mahurkar Anup verfasserin aut Egan Amy verfasserin aut Silva Joana C verfasserin aut In BMC Bioinformatics BMC, 2003 9(2008), 1, p 524 (DE-627)326644814 (DE-600)2041484-5 14712105 nnns volume:9 year:2008 number:1, p 524 https://doi.org/10.1186/1471-2105-9-524 kostenfrei https://doaj.org/article/fee0c8ac514f40148d89f74af69cc530 kostenfrei http://www.biomedcentral.com/1471-2105/9/524 kostenfrei https://doaj.org/toc/1471-2105 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 1, p 524
language	English
source	In BMC Bioinformatics 9(2008), 1, p 524 volume:9 year:2008 number:1, p 524
sourceStr	In BMC Bioinformatics 9(2008), 1, p 524 volume:9 year:2008 number:1, p 524
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Computer applications to medicine. Medical informatics Biology (General)
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container_title	BMC Bioinformatics
authorswithroles_txt_mv	Carlton Jane M @@aut@@ Badger Jonathan H @@aut@@ Crabtree Jonathan @@aut@@ Mahurkar Anup @@aut@@ Egan Amy @@aut@@ Silva Joana C @@aut@@
publishDateDaySort_date	2008-01-01T00:00:00Z
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callnumber-first	R - Medicine
author	Carlton Jane M
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title	IDEA: Interactive Display for Evolutionary Analyses
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title_full	IDEA: Interactive Display for Evolutionary Analyses
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author_browse	Carlton Jane M Badger Jonathan H Crabtree Jonathan Mahurkar Anup Egan Amy Silva Joana C
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title_sort	idea: interactive display for evolutionary analyses
callnumber	R858-859.7
title_auth	IDEA: Interactive Display for Evolutionary Analyses
abstract	<p<Abstract</p< <p<Background</p< <p<The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are <it<codeml </it<and <it<baseml</it<, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.</p< <p<Results</p< <p<We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with <it<codeml </it<and <it<baseml </it<for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.</p< <p<Conclusion</p< <p<IDEA provides a graphical user interface that allows the user to follow a <it<codeml </it<or <it<baseml </it<analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.</p<
abstractGer	<p<Abstract</p< <p<Background</p< <p<The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are <it<codeml </it<and <it<baseml</it<, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.</p< <p<Results</p< <p<We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with <it<codeml </it<and <it<baseml </it<for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.</p< <p<Conclusion</p< <p<IDEA provides a graphical user interface that allows the user to follow a <it<codeml </it<or <it<baseml </it<analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.</p<
abstract_unstemmed	<p<Abstract</p< <p<Background</p< <p<The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are <it<codeml </it<and <it<baseml</it<, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.</p< <p<Results</p< <p<We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with <it<codeml </it<and <it<baseml </it<for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.</p< <p<Conclusion</p< <p<IDEA provides a graphical user interface that allows the user to follow a <it<codeml </it<or <it<baseml </it<analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.</p<
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score	7.3986425

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