CONSEL pipeline

CONSEL specifications

Information


Unique identifier OMICS_24620
Name CONSEL
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Maintained No

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Publication for CONSEL

CONSEL citations

 (7)
2015
PMCID: 4555849

[…] to estimating site-specific likelihood values in the case of the standard, sequence based versions of these tests. once these input tree specific likelihood values are available, they can be used in consel [45] to calculate the au and other tests. samples of 100 random (super)trees were generated (using paup4b10), their likelihoods estimated (using the l.u.st package [35]) and compared […]

2015
PMCID: 5054896

[…] data set 8: –psbc, 8,400 bp; data set 9, –psaa, 8,287 bp; data set 10, –cox1, 8,488 bp. the comparisons of the ml tree topologies (au test) were performed using raxml v. 7.2.8 (stamatakis 2006) and consel (shimodaira and hasegawa 2001). bayesian analysis was run using mrbayes v. 3.2.2 (ronquist et al. 2012). with the aid of the kakusan4 program (tanabe 2011), the best‐fit evolutionary model […]

2012
PMCID: 3458831

[…] monophyly and relationships, we compared the best resulting ml topology to topologies constrained to fit alternative hypotheses using the approximately unbiased test (au) [39] in the program consel [40]. constraint topologies were estimated in raxml with the −g constraint option using the best scoring tree for topology tests estimated from 200 ml searches starting from random tree […]

2011
PMCID: 3242501

[…] randomly concatenating 3, 6, or 9 corresponding genes. the site-by-site likelihoods for the trees were calculated with puzzle (strimmer and von haeseler 1996), the au test was then implemented using consel (shimodaira and hasegawa 2001) to assign the tree probabilities., the network-like relationship was constructed using the splitstree program with neighbor-net distance transformation (huson […]

2010
PMCID: 2958919

[…] and with 6 categories for a discrete gamma model of among-site rate variation. trees obtained by nhphyml-discrete were then compared using the approximately unbiased test [52] implemented in consel [53]., jaccard distances were calculated from the aflp data using phyltools version 1.32 [54]. these distances were used to reconstruct neighbor-joining trees with phylip version 3.66 [55] […]

CONSEL institution(s)
The Institute of Statistical Mathematics, Minatoku, Tokyo, Japan
CONSEL funding source(s)
Supported by Grant-in-Aids from JSPS (12780179, 12554037), and from MEXT (11NP0201).

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