Clann pipeline

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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Documentation


Maintainer


  • person_outline Chris Creevey <>

Publication for Clann

Clann IN pipelines

 (3)
2013
PMCID: 3907059
PMID: 24188869
DOI: 10.1093/molbev/mst212

[…] and eubacterial sequences. the internal branch yielding the maximum ratio of archaebacteria to eubacteria content in the resulting clades was determined with the mrp function implemented in clann 3.2.2 (creevey and mcinerney 2005) using spearman’s rank correlation coefficient. the yeast gene was classified as of eubacterial or archaebacterial ancestry depending on the clade within […]

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

[…] [47] and protein trees were built using the phylip [48] package. the best supertree was found using the most similar supertree (dfit) and maximum quartet fit (qfit) analysis methods from the clann package [49]., oos primaryauthor, experimental design and contributed to all experiments. joc reviewed, sugar metabolism work and intellectual contribution to the manuscript. asv contributed […]

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

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