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Treephyler specifications

Information


Unique identifier OMICS_01469
Name Treephyler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Nucleotide or protein sequences.
Input format FASTA
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Documentation


Publication for Treephyler

Treephyler citations

 (6)
library_books

Classification of Metagenomics Data at Lower Taxonomic Level Using a Robust Supervised Classifier

2015
Evol Bioinform Online
PMCID: 4309676
PMID: 25673967
DOI: 10.4137/EBO.S20523

[…] binning.Existing methods for taxonomic classification fall into two main categories: similarity-based methods and composition- based methods. Similarity-based methods, such as BLAST,2 CARMA,3 MEGAN,4 TreePhyler,5 MLTreeMap,6 and MetaDomain,7 can be used to identify evolutionary relationships of DNA fragments in comparison to a database of reference sequences. But similarity-based methods usually c […]

library_books

Metagenomic search strategies for interactions among plants and multiple microbes

2014
Front Plant Sci
PMCID: 4052219
PMID: 24966863
DOI: 10.3389/fpls.2014.00268

[…] BLASTx option (). Alternatively, databases of conserved protein sequences, such as Pfam, have been searched with translated queries using a Hidden Markov Model in software tools such as CARMA () and Treephyler (). Alphabet reduction (; ) can further accelerate the amino acid sequence approaches. In these cases, non-coding sequences would be prevented from taking part in the taxonomic assignment o […]

library_books

Analysis of composition based metagenomic classification

2012
BMC Genomics
PMCID: 3477002
PMID: 23095761
DOI: 10.1186/1471-2164-13-S5-S1

[…] d Markov modes (IMM) to classify reads with at least 100 bp, TACOA [] merges the k-nearest-neighbor (k-NN) algorithm with kernelized learning strategies to handle sequences from 800 bp to 50 kbp, and Treephyler [] uses hidden Markov models (HMM) to classify reads of 200 bp.This work focuses on composition-based classification using n-mer frequencies to encode genomic sequences. Such an approach in […]

library_books

Current opportunities and challenges in microbial metagenome analysis—a bioinformatic perspective

2012
Brief Bioinform
PMCID: 3504927
PMID: 22966151
DOI: 10.1093/bib/bbs039

[…] algorithm of MEGAN [, ] or the Darkhorse [] and Kirsten [] algorithms.A second possibility is to infer taxonomic information from HMMer searches against Pfam models [] as implemented in CARMA [, ] or Treephyler []. The principle of CARMA is to align a sequence hitting a Pfam model with the model’s curated seed alignment, construct a neighbor-joining tree from the alignment and use this tree to inf […]

library_books

A comparative evaluation of sequence classification programs

2012
BMC Bioinformatics
PMCID: 3428669
PMID: 22574964
DOI: 10.1186/1471-2105-13-92

[…] ignments provided. Thus, we performed a 6-frame translation of our DNA input sequences, and used the UFO web server to assign protein sequences to Pfam domains. These files were then used as input to Treephyler.3. Treephyler is capable of utilizing multiple processing cores during analysis.The only simulated data set associated with the MLTreeMap and Treephyler publications is the simulated medium […]

library_books

Unsupervised Two Way Clustering of Metagenomic Sequences

2012
PMCID: 3336163
PMID: 22577288
DOI: 10.1155/2012/153647

[…] a difficult problem and has been addressed by []. Previously, 16 s/18 s rDNA have been used for phylotyping and assessing species diversity using a rarefaction curve []. Tools such as MetaPhyler and TreePhyler can be used for making an educated guess of the number of species [, ]. Estimating species diversity is still an active area of research, and we do not address it in this paper.Experiments […]

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Treephyler institution(s)
Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany; Department of Earth and Environmental Sciences and GeoBioCenterLMU, Ludwig-Maximilians-Universität München, München, Germany; Abteilung Genomische und Angewandte Mikrobiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität, Göttingen, Germany
Treephyler funding source(s)
This work was supported by DFG (German Research Foundation) Priority Program SPP1174 ‘Deep Metazoan Phylogeny’ (Project Wo896/6-1,2).

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