Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make
Matrix representation with parsimony (MRP) can be used to combine trees in the supertree or the consensus settings. However, despite its popularity, it is still unclear whether MRP is really a consensus method or whether it behaves more like the total evidence approach. Previous simulations have sho...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2006-01-01
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| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.1177/117693430600200018 |
| _version_ | 1818131634949455872 |
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| author | Claudine Levasseur François-Joseph Lapointe |
| author_facet | Claudine Levasseur François-Joseph Lapointe |
| author_sort | Claudine Levasseur |
| collection | DOAJ |
| description | Matrix representation with parsimony (MRP) can be used to combine trees in the supertree or the consensus settings. However, despite its popularity, it is still unclear whether MRP is really a consensus method or whether it behaves more like the total evidence approach. Previous simulations have shown that it approximates total evidence trees, whereas other studies have depicted similarities with average consensus trees. In this paper, we assess the hypothesis that MRP is equally related to both approaches. We conducted a simulation study to evaluate the accuracy of total evidence with that or various consensus methods, including MRP. Our results show that the total evidence trees are not significantly more accurate than average consensus trees that accounts for branch lengths, but that both perform better than MRP trees in the consensus setting. The accuracy rate of all methods was similarly affected by the number of taxa, the number of partitions, and the heterogeneity of the data. |
| first_indexed | 2024-12-11T08:24:04Z |
| format | Article |
| id | doaj.art-473ef4a152734b979168eecae0689b05 |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-11T08:24:04Z |
| publishDate | 2006-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-473ef4a152734b979168eecae0689b052022-12-22T01:14:36ZengSAGE PublishingEvolutionary Bioinformatics1176-93432006-01-01210.1177/117693430600200018Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances MakeClaudine Levasseur0François-Joseph Lapointe1Département de sciences biologiques, Université de Montréal, QC, Canada.Département de sciences biologiques, Université de Montréal, QC, Canada.Matrix representation with parsimony (MRP) can be used to combine trees in the supertree or the consensus settings. However, despite its popularity, it is still unclear whether MRP is really a consensus method or whether it behaves more like the total evidence approach. Previous simulations have shown that it approximates total evidence trees, whereas other studies have depicted similarities with average consensus trees. In this paper, we assess the hypothesis that MRP is equally related to both approaches. We conducted a simulation study to evaluate the accuracy of total evidence with that or various consensus methods, including MRP. Our results show that the total evidence trees are not significantly more accurate than average consensus trees that accounts for branch lengths, but that both perform better than MRP trees in the consensus setting. The accuracy rate of all methods was similarly affected by the number of taxa, the number of partitions, and the heterogeneity of the data.https://doi.org/10.1177/117693430600200018 |
| spellingShingle | Claudine Levasseur François-Joseph Lapointe Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make Evolutionary Bioinformatics |
| title | Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make |
| title_full | Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make |
| title_fullStr | Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make |
| title_full_unstemmed | Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make |
| title_short | Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make |
| title_sort | total evidence average consensus and matrix representation with parsimony what a difference distances make |
| url | https://doi.org/10.1177/117693430600200018 |
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