Clann protocols

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Clann specifications

Information


Unique identifier OMICS_13073
Name Clann
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 3.2.3
Stability Stable
Source code URL https://codeload.github.com/ChrisCreevey/clann/legacy.zip/master
Maintained Yes

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Maintainer


  • person_outline Chris Creevey <>

Publication for Clann

Clann in pipelines

 (3)
2014
PMCID: 4229327
PMID: 24986151
DOI: 10.1111/1751-7915.12141

[…] cluster that contained an rdp sequence., to produce a tree that only contained the otus from the de novo datasets, all other otus were pruned from the tree while preserving the branch lengths, using clann (creevey and mcinerney, ); this tree was visualized using itol (letunic and bork, ) and is shown in fig. . a second phylogeny of only the bacteriodetes, containing the otus from both the de […]

2011
PMCID: 3153122
PMID: 21863127
DOI: 10.4137/EBO.S6861

[…] ii) c3 total (kh test), iii) m2-c3 trimmed (m2-phyml), iv) c2 trimmed (kh test). all trees were constructed with phyml 2.4.4., figure s2. neighbor-joining supertree of protozoan species built with clann 3.1.3 using the total and trimmed (using trimal) alignments., table s1. universal orthologs mapped to kogs found in protozoan., table s2. refseq accession numbers of the protozoan sequences […]

2009
PMCID: 2660350
PMID: 19265535
DOI: 10.1186/1471-2180-9-50

[…] clustalw [] and protein trees were built using the phylip [] package. the best supertree was found using the most similar supertree (dfit) and maximum quartet fit (qfit) analysis methods from the clann package []., oos primaryauthor, experimental design and contributed to all experiments. joc reviewed, sugar metabolism work and intellectual contribution to the manuscript. asv contributed […]


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Clann in publications

 (37)
PMCID: 5890160
PMID: 29662474
DOI: 10.3389/fmicb.2018.00512

[…] trees, was constructed on the basis of the five individual gene phylogenies by means of matrix representation using parsimony (mrp) method (loomis and smith, ; baum, ; ragan, ) as implemented in clann 3.2.3 (creevey and mcinerney, ) setting parameters by default., total lipids were extracted with chloroform/methanol using the extraction method described by bligh and dyer (), as modified […]

PMCID: 5838210
PMID: 29383564
DOI: 10.1007/s12539-018-0282-7

[…] phylogenetic tree is always generated and the corresponding newick tree file saved, a robust tree for the relationship of the species analyzed could be easily created using applications such as clann [], which would then allow for the construction of supertrees from partially overlapping species datasets. moreover, adops projects always provide the nucleotide and protein sequences in fasta […]

PMCID: 5390094
PMID: 28435885
DOI: 10.1128/mSphere.00095-17

[…] for single-copy and multicopy gene phylogenies by prottest. download table¬†s2, docx file, 0.01 mb., all 2,280 orthologous single-copy gene phylogenies (35,622 genes in total) were used as input for clann (), which implements a matrix representation using parsimony (mrp) method to determine consensus phylogeny for many source phylogenies with overlapping taxa or missing taxa. an mrp supertree […]

PMCID: 5522724
PMID: 28740753
DOI: 10.7717/peerj.3578

[…] () is the easiest way to generate such binary matrix. however, it can be prepared even manually using the text¬†editor., the average consensus tables are calculated following the default settings of clann version 4.1.5 (http://chriscreevey.github.io/clann/) (; ; ) for the avcon command with the branch lengths of the all input trees assigned to unity () and also used as future inputs for paup* […]

PMCID: 4798954
PMID: 26952212
DOI: 10.7554/eLife.12704.026

[…] via 100 bootstrap replicates. this set of analyses were performed using raxml instead of phyml because inclusion of premature stop residues are forbidden in phyml., supertrees were generated using clann (ver. 3.2.3) (; ) with six total input trees: three based on ca sequence and three based on gag (- p12) sequence. these ca and gag inputs include two ml phylogenies, one generated using […]


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Clann institution(s)
Bioinformatics and Pharmacogenomics Laboratory, Department of Biology, National University of Ireland Maynooth, Co Kildare, Ireland

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