Skip to main content

Table 1 This table shows a comparison of the tree produced by Dollo-CDP-fast and a best-scoring tree found by the fast heuristic search (FastH)

From: Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem

# of

Same

Dollo-CDP-fast Better

characters

# reps

# reps (\(\Delta\) score)

50 taxa

 500

16

9 (2)

 1000

11

14 (2)

 5000

12

13 (7)

 10000

14

11 (16)

 50000

13

12 (54)

100 taxa

 500

25

0 (NA)

 1000

22

3 (1)

 5000

0

25 (6)

 10000

2

23 (13)

 50000

4

21 (43)

200 taxa

 500

25

0 (NA)

 1000

25

0 (NA)

 5000

6

19 (2)

 10000

4

21 (3)

 50000

0

25 (27)

  1. We report the number of replicates for which Dollo-CDP-fast is the same or better than FastH in terms of Dollo criterion score. For the replicates for which Dollo-CDP-fast is better, we also report the average absolute difference in scores between the trees (rounded to the nearest integer). Recall that Dollo-CDP-fast is given trees produced by FastH as constraints; thus Dollo-CDP-fast is strictly slower in runtime and at least as good in score (we confirmed this was the case in our experiments)
Back to article page

Algorithms for Molecular Biology

ISSN: 1748-7188