dorsal/arxiv
View SchemaUsing the tangle: a consistent construction of phylogenetic distance matrices for quartets
| Authors | J G Sumner, P D Jarvis |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0510035 |
| URL | https://arxiv.org/abs/q-bio/0510035 |
Abstract
Distance based algorithms are a common technique in the construction of phylogenetic trees from taxonomic sequence data. The first step in the implementation of these algorithms is the calculation of a pairwise distance matrix to give a measure of the evolutionary change between any pair of the extant taxa. A standard technique is to use the log det formula to construct pairwise distances from aligned sequence data. We review a distance measure valid for the most general models, and show how the log det formula can be used as an estimator thereof. We then show that the foundation upon which the log det formula is constructed can be generalized to produce a previously unknown estimator which improves the consistency of the distance matrices constructed from the log det formula. This distance estimator provides a consistent technique for constructing quartets from phylogenetic sequence data under the assumption of the most general Markov model of sequence evolution.
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"abstract": "Distance based algorithms are a common technique in the construction of\nphylogenetic trees from taxonomic sequence data. The first step in the\nimplementation of these algorithms is the calculation of a pairwise distance\nmatrix to give a measure of the evolutionary change between any pair of the\nextant taxa. A standard technique is to use the log det formula to construct\npairwise distances from aligned sequence data. We review a distance measure\nvalid for the most general models, and show how the log det formula can be used\nas an estimator thereof. We then show that the foundation upon which the log\ndet formula is constructed can be generalized to produce a previously unknown\nestimator which improves the consistency of the distance matrices constructed\nfrom the log det formula. This distance estimator provides a consistent\ntechnique for constructing quartets from phylogenetic sequence data under the\nassumption of the most general Markov model of sequence evolution.",
"arxiv_id": "q-bio/0510035",
"authors": [
"J G Sumner",
"P D Jarvis"
],
"categories": [
"q-bio.PE"
],
"title": "Using the tangle: a consistent construction of phylogenetic distance matrices for quartets",
"url": "https://arxiv.org/abs/q-bio/0510035"
},
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"variant": "snapshot-2026-03-01",
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