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Fastphylo: fast tools for phylogenetics.

Khan MA, Elias I, Sjölund E, Nylander K, Guimera RV, Schobesberger R, Schmitzberger P, Lagergren J, Arvestad L - BMC Bioinformatics (2013)

Bottom Line: We compare fastphylo with other neighbor joining based methods and report the results in terms of speed and memory efficiency.Fastphylo is a fast, memory efficient, and easy to use software suite.Due to its modular architecture, fastphylo is a flexible tool for many phylogenetic studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: KTH Royal Institute of Technology, Science for Life Laboratory, School of Computer Science and Communication, Department of Computational Biology, Solna, Sweden. malagori@kth.se.

ABSTRACT

Background: Distance methods are ubiquitous tools in phylogenetics. Their primary purpose may be to reconstruct evolutionary history, but they are also used as components in bioinformatic pipelines. However, poor computational efficiency has been a constraint on the applicability of distance methods on very large problem instances.

Results: We present fastphylo, a software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix. We compare fastphylo with other neighbor joining based methods and report the results in terms of speed and memory efficiency.

Conclusions: Fastphylo is a fast, memory efficient, and easy to use software suite. Due to its modular architecture, fastphylo is a flexible tool for many phylogenetic studies.

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Time comparison analysis for dataset-2. Twenty gene families were considered for this analysis, with gene family members ranging from 5,000 to 100,000. The results suggest that fastphylo (fastdist-fnj-pipe) outperforms all the NJ-based tools considered in this study, except RapidNJ. QuickTree took the longest time to compute phylogenetic trees. In the allowed experimental time, i.e. 24 hours, QuickTree was able to compute phylogenetic trees for 7 gene families of size ranging from 5,000 to 35,500 family members, Ninja did it for 9 gene families with family members limited to 45,500, and ClearCut computed trees for 10 gene families (family size limited to 50,000). RapidNJ and fastphylo (fastdist-fnj-pipe), however, computed phylogenetic trees for all the 20 gene families considered in this study, in a reasonable time.
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Figure 5: Time comparison analysis for dataset-2. Twenty gene families were considered for this analysis, with gene family members ranging from 5,000 to 100,000. The results suggest that fastphylo (fastdist-fnj-pipe) outperforms all the NJ-based tools considered in this study, except RapidNJ. QuickTree took the longest time to compute phylogenetic trees. In the allowed experimental time, i.e. 24 hours, QuickTree was able to compute phylogenetic trees for 7 gene families of size ranging from 5,000 to 35,500 family members, Ninja did it for 9 gene families with family members limited to 45,500, and ClearCut computed trees for 10 gene families (family size limited to 50,000). RapidNJ and fastphylo (fastdist-fnj-pipe), however, computed phylogenetic trees for all the 20 gene families considered in this study, in a reasonable time.

Mentions: In order to address the question of how large gene families fastphylo can handle and also to investigate the delay in Figure3, we ran the fastdist-fnj pipe and other NJ tools on dataset-2. The results are formulated in Figures5 and6. Both fastdist-fnj pipe and RapidNJ computed phylogenetic trees for all the 20 gene families of size ranging from 5,000 to 100,000, while ClearCut, Ninja and QuickTree only computed phylogenetic trees for gene families of size ranging from 5,000 up to 50,000, 45,500 and 35,500, respectively, in the allocated time, i.e. 24 hours. The graph in Figure5 reveals that RapidNJ is ∼2 times faster than fastdist-fnj pipe. However, Figure6 shows that the fastdist-fnj pipe uses less memory (a factor of ∼1.5) than RapidNJ.


Fastphylo: fast tools for phylogenetics.

Khan MA, Elias I, Sjölund E, Nylander K, Guimera RV, Schobesberger R, Schmitzberger P, Lagergren J, Arvestad L - BMC Bioinformatics (2013)

Time comparison analysis for dataset-2. Twenty gene families were considered for this analysis, with gene family members ranging from 5,000 to 100,000. The results suggest that fastphylo (fastdist-fnj-pipe) outperforms all the NJ-based tools considered in this study, except RapidNJ. QuickTree took the longest time to compute phylogenetic trees. In the allowed experimental time, i.e. 24 hours, QuickTree was able to compute phylogenetic trees for 7 gene families of size ranging from 5,000 to 35,500 family members, Ninja did it for 9 gene families with family members limited to 45,500, and ClearCut computed trees for 10 gene families (family size limited to 50,000). RapidNJ and fastphylo (fastdist-fnj-pipe), however, computed phylogenetic trees for all the 20 gene families considered in this study, in a reasonable time.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4225504&req=5

Figure 5: Time comparison analysis for dataset-2. Twenty gene families were considered for this analysis, with gene family members ranging from 5,000 to 100,000. The results suggest that fastphylo (fastdist-fnj-pipe) outperforms all the NJ-based tools considered in this study, except RapidNJ. QuickTree took the longest time to compute phylogenetic trees. In the allowed experimental time, i.e. 24 hours, QuickTree was able to compute phylogenetic trees for 7 gene families of size ranging from 5,000 to 35,500 family members, Ninja did it for 9 gene families with family members limited to 45,500, and ClearCut computed trees for 10 gene families (family size limited to 50,000). RapidNJ and fastphylo (fastdist-fnj-pipe), however, computed phylogenetic trees for all the 20 gene families considered in this study, in a reasonable time.
Mentions: In order to address the question of how large gene families fastphylo can handle and also to investigate the delay in Figure3, we ran the fastdist-fnj pipe and other NJ tools on dataset-2. The results are formulated in Figures5 and6. Both fastdist-fnj pipe and RapidNJ computed phylogenetic trees for all the 20 gene families of size ranging from 5,000 to 100,000, while ClearCut, Ninja and QuickTree only computed phylogenetic trees for gene families of size ranging from 5,000 up to 50,000, 45,500 and 35,500, respectively, in the allocated time, i.e. 24 hours. The graph in Figure5 reveals that RapidNJ is ∼2 times faster than fastdist-fnj pipe. However, Figure6 shows that the fastdist-fnj pipe uses less memory (a factor of ∼1.5) than RapidNJ.

Bottom Line: We compare fastphylo with other neighbor joining based methods and report the results in terms of speed and memory efficiency.Fastphylo is a fast, memory efficient, and easy to use software suite.Due to its modular architecture, fastphylo is a flexible tool for many phylogenetic studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: KTH Royal Institute of Technology, Science for Life Laboratory, School of Computer Science and Communication, Department of Computational Biology, Solna, Sweden. malagori@kth.se.

ABSTRACT

Background: Distance methods are ubiquitous tools in phylogenetics. Their primary purpose may be to reconstruct evolutionary history, but they are also used as components in bioinformatic pipelines. However, poor computational efficiency has been a constraint on the applicability of distance methods on very large problem instances.

Results: We present fastphylo, a software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix. We compare fastphylo with other neighbor joining based methods and report the results in terms of speed and memory efficiency.

Conclusions: Fastphylo is a fast, memory efficient, and easy to use software suite. Due to its modular architecture, fastphylo is a flexible tool for many phylogenetic studies.

Show MeSH