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Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

Chernomor O, Minh BQ, von Haeseler A - J. Comput. Biol. (2015)

Bottom Line: Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged.We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace.Hence, partial terrace is the more important factor of timesaving compared to full terrace.

View Article: PubMed Central - PubMed

Affiliation: 1 Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna , Vienna, Austria .

ABSTRACT
In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.

No MeSH data available.


Related in: MedlinePlus

Visualization of NNI neighborhoods and potential computational savings. Each horizontal line reflects the NNI neighborhood for each test alignment, that is 100% of TNNI trees. These neighborhoods are divided into partial terrace bins (Table 2) and depicted here by horizontal segments. The length of each segment corresponds to the mean percentage of TNNI trees falling into the bin (Table 3). Each segment is composed of a green and a red bar, corresponding to the fractions of partition trees that are shared and not shared between T and TNNI, respectively. Basically, green bars indicate potential computational savings when accounting for partial and full terraces during the trees search.
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f8: Visualization of NNI neighborhoods and potential computational savings. Each horizontal line reflects the NNI neighborhood for each test alignment, that is 100% of TNNI trees. These neighborhoods are divided into partial terrace bins (Table 2) and depicted here by horizontal segments. The length of each segment corresponds to the mean percentage of TNNI trees falling into the bin (Table 3). Each segment is composed of a green and a red bar, corresponding to the fractions of partition trees that are shared and not shared between T and TNNI, respectively. Basically, green bars indicate potential computational savings when accounting for partial and full terraces during the trees search.

Mentions: Figure 8 integrates the information from Tables 2 and 3 and provides rough estimates of potential computational savings if accounting for partial and full terraces. The green bars reflect the average percentage of identical induced partition trees when TNNI is compared to T. For example, for DNA1 there is no full terrace, but we observe partial terraces that may lead to a reduction of about 38% (the percentage of green bars) in computation time.


Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

Chernomor O, Minh BQ, von Haeseler A - J. Comput. Biol. (2015)

Visualization of NNI neighborhoods and potential computational savings. Each horizontal line reflects the NNI neighborhood for each test alignment, that is 100% of TNNI trees. These neighborhoods are divided into partial terrace bins (Table 2) and depicted here by horizontal segments. The length of each segment corresponds to the mean percentage of TNNI trees falling into the bin (Table 3). Each segment is composed of a green and a red bar, corresponding to the fractions of partition trees that are shared and not shared between T and TNNI, respectively. Basically, green bars indicate potential computational savings when accounting for partial and full terraces during the trees search.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4663649&req=5

f8: Visualization of NNI neighborhoods and potential computational savings. Each horizontal line reflects the NNI neighborhood for each test alignment, that is 100% of TNNI trees. These neighborhoods are divided into partial terrace bins (Table 2) and depicted here by horizontal segments. The length of each segment corresponds to the mean percentage of TNNI trees falling into the bin (Table 3). Each segment is composed of a green and a red bar, corresponding to the fractions of partition trees that are shared and not shared between T and TNNI, respectively. Basically, green bars indicate potential computational savings when accounting for partial and full terraces during the trees search.
Mentions: Figure 8 integrates the information from Tables 2 and 3 and provides rough estimates of potential computational savings if accounting for partial and full terraces. The green bars reflect the average percentage of identical induced partition trees when TNNI is compared to T. For example, for DNA1 there is no full terrace, but we observe partial terraces that may lead to a reduction of about 38% (the percentage of green bars) in computation time.

Bottom Line: Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged.We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace.Hence, partial terrace is the more important factor of timesaving compared to full terrace.

View Article: PubMed Central - PubMed

Affiliation: 1 Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna , Vienna, Austria .

ABSTRACT
In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.

No MeSH data available.


Related in: MedlinePlus