LSD (Least-Squares Dating) Software: Fast dating using least-squares criteria and algorithms (C++ code)

Thu Hien To; Matthieu Jung; Samantha Lycett; Olivier Gascuel

LSD (Least-Squares Dating) Software: Fast dating using least-squares criteria and algorithms (C++ code)

Thu Hien To (Developer), Matthieu Jung (Developer), Samantha Lycett (Developer), Olivier Gascuel (Developer)

Royal (Dick) School of Veterinary Studies

Research output: Non-textual form › Software

Abstract

Here we present very fast algorithms to estimate the dates and substitution rates on phylogenetic trees when the sequences have been sampled through time. These algorithms are based on a Gaussian model closely related to the Langley-Fitch molecular-clock model. When the input tree is unrooted, they can provide an estimate for the root position, thus representing a new, practical alternative to the standard rooting methods (e.g. mid-point).

These algorithms are implemented in the LSD software (Least-Squares Dating), which can be downloaded from http://www.atgc-montpellier.fr/LSD/, along with all our data sets and detailed results

Original language	English
Publication status	Published - 16 Sept 2015

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http://www.atgc-montpellier.fr/LSD/

1 Article

Fast dating using least-squares criteria and algorithms
To, T. H., Jung, M., Lycett, S. & Gascuel, O., Jan 2016, In: Systematic biology. 65, 1, p. 82-97
Research output: Contribution to journal › Article › peer-review

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title = "LSD (Least-Squares Dating) Software: Fast dating using least-squares criteria and algorithms (C++ code)",

abstract = "Here we present very fast algorithms to estimate the dates and substitution rates on phylogenetic trees when the sequences have been sampled through time. These algorithms are based on a Gaussian model closely related to the Langley-Fitch molecular-clock model. When the input tree is unrooted, they can provide an estimate for the root position, thus representing a new, practical alternative to the standard rooting methods (e.g. mid-point).These algorithms are implemented in the LSD software (Least-Squares Dating), which can be downloaded from http://www.atgc-montpellier.fr/LSD/, along with all our data sets and detailed results",

author = "To, {Thu Hien} and Matthieu Jung and Samantha Lycett and Olivier Gascuel",

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N2 - Here we present very fast algorithms to estimate the dates and substitution rates on phylogenetic trees when the sequences have been sampled through time. These algorithms are based on a Gaussian model closely related to the Langley-Fitch molecular-clock model. When the input tree is unrooted, they can provide an estimate for the root position, thus representing a new, practical alternative to the standard rooting methods (e.g. mid-point).These algorithms are implemented in the LSD software (Least-Squares Dating), which can be downloaded from http://www.atgc-montpellier.fr/LSD/, along with all our data sets and detailed results

AB - Here we present very fast algorithms to estimate the dates and substitution rates on phylogenetic trees when the sequences have been sampled through time. These algorithms are based on a Gaussian model closely related to the Langley-Fitch molecular-clock model. When the input tree is unrooted, they can provide an estimate for the root position, thus representing a new, practical alternative to the standard rooting methods (e.g. mid-point).These algorithms are implemented in the LSD software (Least-Squares Dating), which can be downloaded from http://www.atgc-montpellier.fr/LSD/, along with all our data sets and detailed results

M3 - Software

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LSD (Least-Squares Dating) Software: Fast dating using least-squares criteria and algorithms (C++ code)

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Fast dating using least-squares criteria and algorithms

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