Concaterpillar protocols

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Concaterpillar specifications

Information


Unique identifier OMICS_11501
Name Concaterpillar
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MPI
Computer skills Advanced
Version 1.8
Stability Alpha
Requirements
RAxML, SciPy, mpi4py, Python
Maintained Yes

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Maintainer


  • person_outline Jessica W. Leigh <>

Publication for Concaterpillar

Concaterpillar in pipeline

2015
PMCID: 4407914
PMID: 25495187
DOI: 10.1111/jeb.12570

[…] for stop codons. finally, we removed phylogenetically uninformative insertions as well as questionable alignment positions adjacent to insertions., the marker set was partitioned using the programs concaterpillar (leigh et al., ) and partitionfinder (lanfear et al., ) as described in text s1. bayesian species tree reconstructions were performed with beast v.2.1 (bouckaert et al., ) under a wide […]


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Concaterpillar in publications

 (17)
PMCID: 5890160
PMID: 29662474
DOI: 10.3389/fmicb.2018.00512

[…] with 1,000 replications. only bootstrap values equal or greater than 70% are shown on the trees. topology congruence tests among individual and concatenated gene phylogenies were performed using concaterpillar v. 1.8a software (leigh et al., ) setting the p-value cutoff to 0.05., a supertree, considering all previously obtained individual trees, was constructed on the basis of the five […]

PMCID: 4334724
PMID: 25433288
DOI: 10.1016/j.ympev.2014.10.009

[…] the lamprologini and the ectodini., we first tested for topological incongruence between individual gene trees, using hierarchical likelihood ratio tests as implemented in the software concaterpillar (v1.7.2) (), with default settings and the assumption of linked branch lengths. as part of the concaterpillar analysis, tree inference was performed using raxml (v7.2.8) (), assuming […]

PMCID: 4407914
PMID: 25495187
DOI: 10.1111/jeb.12570

[…] for stop codons. finally, we removed phylogenetically uninformative insertions as well as questionable alignment positions adjacent to insertions., the marker set was partitioned using the programs concaterpillar (leigh et al., ) and partitionfinder (lanfear et al., ) as described in text s1. bayesian species tree reconstructions were performed with beast v.2.1 (bouckaert et al., ) under a wide […]

PMCID: 4395847
PMID: 25634098
DOI: 10.1093/sysbio/syv007

[…] we investigated whether topologies and branch lengths of the individual loci are consistent enough to justify concatenation of the markers by means of a hierarchical likelihood-ratio test in concaterpillar v. 1.5 ()., we created a supermatrix of the 20 nuclear and 2 mitochondrial markers in mesquite. to increase the efficiency of tree searches, optimal partitioning schemes […]

PMCID: 4164646
PMID: 25222863
DOI: 10.1371/journal.pone.0107679

[…] were discussed in yang et al. . therefore, we randomly selected one clone from each species for the further analyses. the incongruence length difference test (ild) , implemented in paup* 4.0b10 , concaterpillar (a hierarchical likelihood ratio test) , and cadm (a test of congruence among distance matrices) were performed to assess congruence between different datasets. according to the three […]


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Concaterpillar institution(s)
Department of Biochemistry and Molecular Biology, Dalhousie University Halifax NS, Canada; Department of Mathematics and Statistics and Genome Atlantic, Dalhousie University Halifax NS, Canada; Department für Biologie I, Botanik, Ludwig-Maximilians-Universität München Menzingerstraße, München, Germany

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