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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 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.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
Time comparison of fastprotvsprotdist. This figure shows the time comparison between fastprot and protdist on 10 protein families with family size ranging from 1,000 to 10,000. The time duration for each experiment was limited to 24 hours. We can see that fastprot clearly outperforms protdist when computing distance matrices for protein families. protdist took 14.07 hours to compute the distance matrix for a protein family of size 2,000 while fastprot computed it in 0.16 hours.
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Figure 2: Time comparison of fastprotvsprotdist. This figure shows the time comparison between fastprot and protdist on 10 protein families with family size ranging from 1,000 to 10,000. The time duration for each experiment was limited to 24 hours. We can see that fastprot clearly outperforms protdist when computing distance matrices for protein families. protdist took 14.07 hours to compute the distance matrix for a protein family of size 2,000 while fastprot computed it in 0.16 hours.

Mentions: fastprot provides more distance functions when compared to other neighbour joining tools considered in this study. Clearcut (version 1.0.9)[9], Ninja (version 1.2.1)[8], and RapidNJ (version 2.1.0) provide JC[17] and JCK[18], QuickTree (version 1.1)[5] provides JCK, while fastprot implements seven distance functions including JC, JCK, WAG[20], JTT[21], DAY[22], MVR[23], and LG[24]. It is more than 200 times faster than protdist, a Phylip program for estimating distance matrices for protein alignments (see Figure2). fastprot also allows longer accessions compared to protdist which has the limitation of ten characters for an accession number.


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 of fastprotvsprotdist. This figure shows the time comparison between fastprot and protdist on 10 protein families with family size ranging from 1,000 to 10,000. The time duration for each experiment was limited to 24 hours. We can see that fastprot clearly outperforms protdist when computing distance matrices for protein families. protdist took 14.07 hours to compute the distance matrix for a protein family of size 2,000 while fastprot computed it in 0.16 hours.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Time comparison of fastprotvsprotdist. This figure shows the time comparison between fastprot and protdist on 10 protein families with family size ranging from 1,000 to 10,000. The time duration for each experiment was limited to 24 hours. We can see that fastprot clearly outperforms protdist when computing distance matrices for protein families. protdist took 14.07 hours to compute the distance matrix for a protein family of size 2,000 while fastprot computed it in 0.16 hours.
Mentions: fastprot provides more distance functions when compared to other neighbour joining tools considered in this study. Clearcut (version 1.0.9)[9], Ninja (version 1.2.1)[8], and RapidNJ (version 2.1.0) provide JC[17] and JCK[18], QuickTree (version 1.1)[5] provides JCK, while fastprot implements seven distance functions including JC, JCK, WAG[20], JTT[21], DAY[22], MVR[23], and LG[24]. It is more than 200 times faster than protdist, a Phylip program for estimating distance matrices for protein alignments (see Figure2). fastprot also allows longer accessions compared to protdist which has the limitation of ten characters for an accession number.

Bottom Line: 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.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