MLTreeMap protocols

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MLTreeMap specifications

Information


Unique identifier OMICS_01457
Name MLTreeMap
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline C. von Mering <>

Publication for MLTreeMap

MLTreeMap in pipeline

2016
PMCID: 5067608
PMID: 27739431
DOI: 10.1038/ncomms12770

[…] classifier version 2.7 (http://rdp.cme.msu.edu/) on 16s rrna genes detected by barrnap version 0.4.2 (http://www.vicbioinformatics.com/software.barrnap.shtml). if no 16s rrna gene was detected, mltreemap version 2.061 (http://mltreemap.org/) annotations were used instead., the ani between the selected draft genomes and references genomes found in ncbi genome database […]


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MLTreeMap in publications

 (10)
PMCID: 5579096
PMID: 28878981
DOI: 10.1098/rsos.170315

[…] all nodes in the reference topology, with the placement likelihood calculated for every combination. the highest scoring placements are retained for evaluation. this approach is implemented in mltreemap [], pplacer [] and evolutionary placement algorithm (epa) []. of the three, only the epa is used in this paper, because ‘there was no clear difference in accuracy between epa and pplacer’ […]

PMCID: 5067608
PMID: 27739431
DOI: 10.1038/ncomms12770

[…] classifier version 2.7 (http://rdp.cme.msu.edu/) on 16s rrna genes detected by barrnap version 0.4.2 (http://www.vicbioinformatics.com/software.barrnap.shtml). if no 16s rrna gene was detected, mltreemap version 2.061 (http://mltreemap.org/) annotations were used instead., the ani between the selected draft genomes and references genomes found in ncbi genome database […]

PMCID: 4309676
PMID: 25673967
DOI: 10.4137/EBO.S20523

[…] 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 […]

PMCID: 4028982
PMID: 24581117
DOI: 10.1186/1471-2164-15-169

[…] on the contigs which are ordered largest to smallest, i.e. peg.1 is the first gene on the largest contig., the contigs were concatenated into a single molecule and analyzed with ml tree (http://mltreemap.org/). this software searches through fully sequenced bacterial genomes for 31 common protein coding marker genes and constructs a phylogenetic tree based on the alignment of the best blast […]

PMCID: 3760913
PMID: 24019895
DOI: 10.1371/journal.pone.0073071

[…] other metagenomics tools for binning/classifying sequencing reads or identifying relative abundance of species. this includes alignment–based approaches (mg–rast , metaphyler , sort–items , marta , mltreemap ), composition–based approaches (phylophytias , clams , phymm ) and a hybrid approach (phymmbl ). here, comparison of the results was difficult as several approaches only perform […]


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MLTreeMap institution(s)
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland

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