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TreeCollapseCL specifications

Information


Unique identifier OMICS_29986
Name TreeCollapseCL
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output format NEXUS/NEWICK,CSV
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Additional information


http://emmahodcroft.com/TreeCollapseCL.html

TreeCollapseCL citations

 (8)
library_books

Multiple Introductions and Recent Spread of the Emerging Human Pathogen Mycobacterium ulcerans across Africa

2017
Genome Biol Evol
PMCID: 5381664
PMID: 28137745
DOI: 10.1093/gbe/evx003

[…] before the RAxML runs. For each run, we performed 10,000 rapid bootstrap analyses to assess support for the ML phylogeny. The tree with the highest likelihood across the 10 runs was selected. We used TreeCollapseCL v4 () to collapse nodes in the tree with bootstrap values below a set threshold of 70% () to polytomies, whereas preserving the length of the tree. Phylogenetic relationships were infer […]

library_books

Disruption of phenylalanine hydroxylase reduces adult lifespan and fecundity, and impairs embryonic development in parthenogenetic pea aphids

2016
Sci Rep
PMCID: 5046115
PMID: 27694983
DOI: 10.1038/srep34321

[…] te classes, 439 informative sites analyzed), and the reliability of each branch was evaluated using the bootstrap method, with 1000 replications. Poorly supported branches (<50%) were collapsed using TreeCollapseCL 4 (http://emmahodcroft.com/TreeCollapseCL.html). […]

call_split

Broad activation of latent HIV 1 in vivo

2016
Nat Commun
PMCID: 5025526
PMID: 27605062
DOI: 10.1038/ncomms12731
call_split See protocol

[…] netic HIV-1 diversity (average pairwise distance) of HIV-1 DNA or RNA sequences were calculated using the p-distance model in MEGA-CC. Branches with less than one bootstrap support were removed using TreeCollapseCL4 (Emma Hodcroft, http://emmahodcroft.com/TreeCollapseCL.html). Bootstrap values greater than 75 are included on the phylogenetic trees. Tree images were generated with ggtree (https://b […]

call_split

Five decades of genome evolution in the globally distributed, extensively antibiotic resistant Acinetobacter baumannii global clone 1

2016
Microb Genom
PMCID: 5320584
PMID: 28348844
DOI: 10.1099/mgen.0.000052
call_split See protocol

[…] m 1000 bootstraps. The tree topology contained only two bipartitions with < 50 % bootstrap support; these bipartitions were collapsed into polytomies (using TreeCollapserCL 4; http://emmahodcroft.com/TreeCollapseCL.html) to form the final ML tree. The tree and Gubbins output are available in FigShare. […]

call_split

Similarity Based Codes Sequentially Assigned to Ebolavirus Genomes Are Informative of Species Membership, Associated Outbreaks, and Transmission Chains

2015
PMCID: 4438903
PMID: 26034773
DOI: 10.1093/ofid/ofv024
call_split See protocol

[…] he GTRGAMMA model. Nonparametric bootstrap branch support values were mapped onto the best log-likelihood ML tree, and clades with less than 50% bootstrap support were collapsed into polytomies using TreeCollapseCL4 []. […]

library_books

The Evolution of Fungal Metabolic Pathways

2014
PLoS Genet
PMCID: 4256263
PMID: 25474404
DOI: 10.1371/journal.pgen.1004816

[…] port in ECgene trees were handled through a multi-step approach. First, ECgene tree branches with less than 0.90 SH-like local support were collapsed using treecollapsercl v4 (http://emmahodcroft.com/TreeCollapseCL.html). This collapsed ECgene tree was rooted and its polytomies resolved against the bifurcating species phylogeny. This resolved ECgene tree was then reconciled to the multifurcating, […]

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TreeCollapseCL institution(s)
Andrew Leigh Brown Group, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK

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