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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.

Show MeSH
Memory comparison analysis for dataset-1. Ten gene families were considered for this analysis, with family size ranging from 1,000 to 10,000. The vertical axis represents memory utilization in GiB’s, while the horizontal axis represents the number of gene sequences per gene family. The results here suggests that ClearCut and RapidNJ use more memory compared to the rest of NJ tools as the family size increases.
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Figure 4: Memory comparison analysis for dataset-1. Ten gene families were considered for this analysis, with family size ranging from 1,000 to 10,000. The vertical axis represents memory utilization in GiB’s, while the horizontal axis represents the number of gene sequences per gene family. The results here suggests that ClearCut and RapidNJ use more memory compared to the rest of NJ tools as the family size increases.

Mentions: Results on dataset-1 is shown in Figures3 and4. Figure3 shows the time comparison analysis, while in Figure4 we show the memory utilization of different NJ tools considered in our study. From the time comparison in Figure3, it is clear that our fastdist-fnj pipe outperforms Clearcut, QuickTree and Ninja, while it shows a slight delay when compared with RapidNJ. To investigate this further, we ran the same experiment on dataset-2 (see section 'Results on dataset-2’).


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)

Memory comparison analysis for dataset-1. Ten gene families were considered for this analysis, with family size ranging from 1,000 to 10,000. The vertical axis represents memory utilization in GiB’s, while the horizontal axis represents the number of gene sequences per gene family. The results here suggests that ClearCut and RapidNJ use more memory compared to the rest of NJ tools as the family size increases.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Memory comparison analysis for dataset-1. Ten gene families were considered for this analysis, with family size ranging from 1,000 to 10,000. The vertical axis represents memory utilization in GiB’s, while the horizontal axis represents the number of gene sequences per gene family. The results here suggests that ClearCut and RapidNJ use more memory compared to the rest of NJ tools as the family size increases.
Mentions: Results on dataset-1 is shown in Figures3 and4. Figure3 shows the time comparison analysis, while in Figure4 we show the memory utilization of different NJ tools considered in our study. From the time comparison in Figure3, it is clear that our fastdist-fnj pipe outperforms Clearcut, QuickTree and Ninja, while it shows a slight delay when compared with RapidNJ. To investigate this further, we ran the same experiment on dataset-2 (see section 'Results on dataset-2’).

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