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11 results for “invariant sites”
Data from: Complex models of sequence evolution require accurate estimators as exemplified with the invariable site plus Gamma model
The invariable site plus Γ model is widely used to model rate heterogeneity among alignment sites in maximum likelihood and Bayesian phylogenetic analyses. The proof that the invariable site plus continuous Γ model is identifiable (model parameters can be inferred correctly given enough data) has increased the creditability of its application to phylogeny reconstruction. However, most phylogenetic software implement the invariable site plus discrete Γ model, whose identifiability is likely but unproven. How well the parameters of the invariable site plus discrete Γ model are estimated is still disputed. Especially the correlation of the fraction of invariable sites with the fractions of sites with a slow evolutionary rate is discussed as being problematic. We show that optimization heuristics as implemented in frequently used phylogenetic software cannot always reliably estimate the shape parameter, the proportion of invariable sites and the tree length. Here, we propose an improved optimization heuristic that accurately estimates the three parameters. While research efforts mainly focus on tree search methods, our results signify the equal importance of verifying and developing effective estimation methods for complex models of sequence evolution.
Data from: Invariant versus classical quartet inference when evolution is heterogeneous across sites and lineages
One reason why classical phylogenetic reconstruction methods fail to correctly infer the underlying topology is because they assume oversimplified models. In this paper we propose a quartet reconstruction method consistent with the most general Markov model of nucleotide substitution, which can also deal with data coming from mixtures on the same topology. Our proposed method uses phylogenetic invariants and provides a system of weights that can be used as input for quartet-based methods. We study its performance on real data and on a wide range of simulated 4-taxon data (both time-homogeneous and nonhomogeneous, with or without among-site rate heterogeneity, and with different branch length settings). We compare it to the classical methods of neighbor-joining (with paralinear distance), maximum likelihood (with different underlying models), and maximum parsimony. Our results show that this method is accurate and robust, has a similar performance to ML when data satisfies the assumptions of both methods, and outperforms the other methods when these are based on inappropriate substitution models. If alignments are long enough, then it also outperforms other methods when some of its assumptions are violated.
Data from: Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant
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Data from: Complex models of sequence evolution require accurate estimators as exemplified with the invariable site plus Gamma model
Open the record for dataset details and reuse information.
Data from: Invariant versus classical quartet inference when evolution is heterogeneous across sites and lineages
Open the record for dataset details and reuse information.
CEOS Cal Val Test Site - Mauritania 1 - Pseudo-Invariant Calibration Site (PICS)
On the background of these requirements for sensor calibration, intercalibration and product validation, the subgroup on Calibration and Validation of the Committee on Earth Observing System (CEOS) formulated the following recommendation during the plenary session held in China at the end of 2004, with the goal of setting-up and operating an internet based system to provide sensor data, protocols and guidelines for these purposes: Background: Reference Datasets are required to support the understanding of climate change and quality assure operational services by Earth Observing satellites. The data from different sensors and the resulting synergistic data products require a high level of accuracy that can only be obtained through continuous traceable calibration and validation activities. Requirement: Initiate an activity to document a reference methodology to predict Top of Atmosphere (TOA) radiance for which currently flying and planned wide swath sensors can be intercompared, i.e. define a standard for traceability. Also create and maintain a fully accessible web page containing, on an instrument basis, links to all instrument characteristics needed for intercomparisons as specified above, ideally in a common format. In addition, create and maintain a database (e.g. SADE) of instrument data for specific vicarious calibration sites, including site characteristics, in a common format. Each agency is responsible for providing data for their instruments in this common format. Recommendation : The required activities described above should be supported for an implementation period of two years and a maintenance period over two subsequent years. The CEOS should encourage a member agency to accept the lead role in supporting this activity. CEOS should request all member agencies to support this activity by providing appropriate information and data in a timely manner. Pseudo-Invariant Calibration Sites (PICS): Mauritania 1 is one of six CEOS reference Pseudo-Invariant Calibration Sites (PICS) that are CEOS Reference Test Sites. Besides the nominally good site characteristics (temporal stability, uniformity, homogeneity, etc.), these six PICS were selected by also taking into account their heritage and the large number of datasets from multiple instruments that already existed in the EO archives and the long history of characterization performed over these sites. The PICS have high reflectance and are usually made up of sand dunes with climatologically low aerosol loading and practically no vegetation. Consequently, these PICS can be used to evaluate the long-term stability of instrument and facilitate inter-comparison of multiple instruments.
CEOS Cal Val Test Site - Algeria 3 - Pseudo-Invariant Calibration Site (PICS)
On the background of these requirements for sensor calibration, intercalibration and product validation, the subgroup on Calibration and Validation of the Committee on Earth Observing System (CEOS) formulated the following recommendation during the plenary session held in China at the end of 2004, with the goal of setting-up and operating an internet based system to provide sensor data, protocols and guidelines for these purposes: Background: Reference Datasets are required to support the understanding of climate change and quality assure operational services by Earth Observing satellites. The data from different sensors and the resulting synergistic data products require a high level of accuracy that can only be obtained through continuous traceable calibration and validation activities. Requirement: Initiate an activity to document a reference methodology to predict Top of Atmosphere (TOA) radiance for which currently flying and planned wide swath sensors can be intercompared, i.e. define a standard for traceability. Also create and maintain a fully accessible web page containing, on an instrument basis, links to all instrument characteristics needed for intercomparisons as specified above, ideally in a common format. In addition, create and maintain a database (e.g. SADE) of instrument data for specific vicarious calibration sites, including site characteristics, in a common format. Each agency is responsible for providing data for their instruments in this common format. Recommendation : The required activities described above should be supported for an implementation period of two years and a maintenance period over two subsequent years. The CEOS should encourage a member agency to accept the lead role in supporting this activity. CEOS should request all member agencies to support this activity by providing appropriate information and data in a timely manner. Pseudo-Invariant Calibration Sites (PICS): Algeria 3 is one of six CEOS reference Pseudo-Invariant Calibration Sites (PICS) that are CEOS Reference Test Sites. Besides the nominally good site characteristics (temporal stability, uniformity, homogeneity, etc.), these six PICS were selected by also taking into account their heritage and the large number of datasets from multiple instruments that already existed in the EO archives and the long history of characterization performed over these sites. The PICS have high reflectance and are usually made up of sand dunes with climatologically low aerosol loading and practically no vegetation. Consequently, these PICS can be used to evaluate the long-term stability of instrument and facilitate inter-comparison of multiple instruments.
CEOS Cal Val Test Site - Libya 4 - Pseudo-Invariant Calibration Site (PICS)
On the background of these requirements for sensor calibration, intercalibration and product validation, the subgroup on Calibration and Validation of the Committee on Earth Observing System (CEOS) formulated the following recommendation during the plenary session held in China at the end of 2004, with the goal of setting-up and operating an internet based system to provide sensor data, protocols and guidelines for these purposes: Background: Reference Datasets are required to support the understanding of climate change and quality assure operational services by Earth Observing satellites. The data from different sensors and the resulting synergistic data products require a high level of accuracy that can only be obtained through continuous traceable calibration and validation activities. Requirement: Initiate an activity to document a reference methodology to predict Top of Atmosphere (TOA) radiance for which currently flying and planned wide swath sensors can be intercompared, i.e. define a standard for traceability. Also create and maintain a fully accessible web page containing, on an instrument basis, links to all instrument characteristics needed for intercomparisons as specified above, ideally in a common format. In addition, create and maintain a database (e.g. SADE) of instrument data for specific vicarious calibration sites, including site characteristics, in a common format. Each agency is responsible for providing data for their instruments in this common format. Recommendation : The required activities described above should be supported for an implementation period of two years and a maintenance period over two subsequent years. The CEOS should encourage a member agency to accept the lead role in supporting this activity. CEOS should request all member agencies to support this activity by providing appropriate information and data in a timely manner. Pseudo-Invariant Calibration Sites (PICS): Libya 4 is one of six CEOS reference Pseudo-Invariant Calibration Sites (PICS) that are CEOS Reference Test Sites. Besides the nominally good site characteristics (temporal stability, uniformity, homogeneity, etc.), these six PICS were selected by also taking into account their heritage and the large number of datasets from multiple instruments that already existed in the EO archives and the long history of characterization performed over these sites. The PICS have high reflectance and are usually made up of sand dunes with climatologically low aerosol loading and practically no vegetation. Consequently, these PICS can be used to evaluate the long-term stability of instrument and facilitate inter-comparison of multiple instruments.
CEOS Cal Val Test Site - Mauritania 2 - Pseudo-Invariant Calibration Site (PICS)
On the background of these requirements for sensor calibration, intercalibration and product validation, the subgroup on Calibration and Validation of the Committee on Earth Observing System (CEOS) formulated the following recommendation during the plenary session held in China at the end of 2004, with the goal of setting-up and operating an internet based system to provide sensor data, protocols and guidelines for these purposes: Background: Reference Datasets are required to support the understanding of climate change and quality assure operational services by Earth Observing satellites. The data from different sensors and the resulting synergistic data products require a high level of accuracy that can only be obtained through continuous traceable calibration and validation activities. Requirement: Initiate an activity to document a reference methodology to predict Top of Atmosphere (TOA) radiance for which currently flying and planned wide swath sensors can be intercompared, i.e. define a standard for traceability. Also create and maintain a fully accessible web page containing, on an instrument basis, links to all instrument characteristics needed for intercomparisons as specified above, ideally in a common format. In addition, create and maintain a database (e.g. SADE) of instrument data for specific vicarious calibration sites, including site characteristics, in a common format. Each agency is responsible for providing data for their instruments in this common format. Recommendation : The required activities described above should be supported for an implementation period of two years and a maintenance period over two subsequent years. The CEOS should encourage a member agency to accept the lead role in supporting this activity. CEOS should request all member agencies to support this activity by providing appropriate information and data in a timely manner. Pseudo-Invariant Calibration Sites (PICS): Mauritania 2 is one of six CEOS reference Pseudo-Invariant Calibration Sites (PICS) that are CEOS Reference Test Sites. Besides the nominally good site characteristics (temporal stability, uniformity, homogeneity, etc.), these six PICS were selected by also taking into account their heritage and the large number of datasets from multiple instruments that already existed in the EO archives and the long history of characterization performed over these sites. The PICS have high reflectance and are usually made up of sand dunes with climatologically low aerosol loading and practically no vegetation. Consequently, these PICS can be used to evaluate the long-term stability of instrument and facilitate inter-comparison of multiple instruments.
CEOS Cal Val Test Site - Libya 1 - Pseudo-Invariant Calibration Site (PICS)
On the background of these requirements for sensor calibration, intercalibration and product validation, the subgroup on Calibration and Validation of the Committee on Earth Observing System (CEOS) formulated the following recommendation during the plenary session held in China at the end of 2004, with the goal of setting-up and operating an internet based system to provide sensor data, protocols and guidelines for these purposes: Background: Reference Datasets are required to support the understanding of climate change and quality assure operational services by Earth Observing satellites. The data from different sensors and the resulting synergistic data products require a high level of accuracy that can only be obtained through continuous traceable calibration and validation activities. Requirement: Initiate an activity to document a reference methodology to predict Top of Atmosphere (TOA) radiance for which currently flying and planned wide swath sensors can be intercompared, i.e. define a standard for traceability. Also create and maintain a fully accessible web page containing, on an instrument basis, links to all instrument characteristics needed for intercomparisons as specified above, ideally in a common format. In addition, create and maintain a database (e.g. SADE) of instrument data for specific vicarious calibration sites, including site characteristics, in a common format. Each agency is responsible for providing data for their instruments in this common format. Recommendation : The required activities described above should be supported for an implementation period of two years and a maintenance period over two subsequent years. The CEOS should encourage a member agency to accept the lead role in supporting this activity. CEOS should request all member agencies to support this activity by providing appropriate information and data in a timely manner. Pseudo-Invariant Calibration Sites (PICS): Libya 4 is one of six CEOS reference Pseudo-Invariant Calibration Sites (PICS) that are CEOS Reference Test Sites. Besides the nominally good site characteristics (temporal stability, uniformity, homogeneity, etc.), these six PICS were selected by also taking into account their heritage and the large number of datasets from multiple instruments that already existed in the EO archives and the long history of characterization performed over these sites. The PICS have high reflectance and are usually made up of sand dunes with climatologically low aerosol loading and practically no vegetation. Consequently, these PICS can be used to evaluate the long-term stability of instrument and facilitate inter-comparison of multiple instruments.
CEOS Cal Val Test Site - Algeria 5 - Pseudo-Invariant Calibration Site (PICS)
On the background of these requirements for sensor calibration, intercalibration and product validation, the subgroup on Calibration and Validation of the Committee on Earth Observing System (CEOS) formulated the following recommendation during the plenary session held in China at the end of 2004, with the goal of setting-up and operating an internet based system to provide sensor data, protocols and guidelines for these purposes: Background: Reference Datasets are required to support the understanding of climate change and quality assure operational services by Earth Observing satellites. The data from different sensors and the resulting synergistic data products require a high level of accuracy that can only be obtained through continuous traceable calibration and validation activities. Requirement: Initiate an activity to document a reference methodology to predict Top of Atmosphere (TOA) radiance for which currently flying and planned wide swath sensors can be intercompared, i.e. define a standard for traceability. Also create and maintain a fully accessible web page containing, on an instrument basis, links to all instrument characteristics needed for intercomparisons as specified above, ideally in a common format. In addition, create and maintain a database (e.g. SADE) of instrument data for specific vicarious calibration sites, including site characteristics, in a common format. Each agency is responsible for providing data for their instruments in this common format. Recommendation : The required activities described above should be supported for an implementation period of two years and a maintenance period over two subsequent years. The CEOS should encourage a member agency to accept the lead role in supporting this activity. CEOS should request all member agencies to support this activity by providing appropriate information and data in a timely manner. Pseudo-Invariant Calibration Sites (PICS): Algeria 5 is one of six CEOS reference Pseudo-Invariant Calibration Sites (PICS) that are CEOS Reference Test Sites. Besides the nominally good site characteristics (temporal stability, uniformity, homogeneity, etc.), these six PICS were selected by also taking into account their heritage and the large number of datasets from multiple instruments that already existed in the EO archives and the long history of characterization performed over these sites. The PICS have high reflectance and are usually made up of sand dunes with climatologically low aerosol loading and practically no vegetation. Consequently, these PICS can be used to evaluate the long-term stability of instrument and facilitate inter-comparison of multiple instruments.
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