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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

Versioning


No version available

Documentation


Maintainer


  • person_outline Chris Creevey

Publication for Clann

Clann citations

 (38)
library_books

Genotypic and Lipid Analyses of Strains From the Archaeal Genus Halorubrum Reveal Insights Into Their Taxonomy, Divergence, and Population Structure

2018
Front Microbiol
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 […]

library_books

Large Scale Analyses and Visualization of Adaptive Amino Acid Changes Projects

2018
Interdiscip Sci
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 […]

library_books

Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes

2017
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 […]

library_books

A laid back trip through the Hennigian Forests

2017
PeerJ
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* […]

library_books

Tracking interspecies transmission and long term evolution of an ancient retrovirus using the genomes of modern mammals

2016
eLife
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 […]

library_books

Genus Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin

2015
PLoS Genet
PMCID: 4634964
PMID: 26539826
DOI: 10.1371/journal.pgen.1005614

[…] = 1 ngen = 300000”. we also merged individual ml gene trees for cegs into a supertree []. individual gene trees were constructed using the same approach and they were merged into a supertree using clann []. using this approach, more genes could be incorporated into the final tree, as missing a strain in a gene tree could be tolerated. both approaches yielded the same phylogeny […]


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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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