TreeBASE Search-Analyses for study 11985

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Analyses for Study 11985

Citation title: "The diversification of Aspidoderidae (Nematoda) linked to four events of host-switching in mammals".

Study name: "The diversification of Aspidoderidae (Nematoda) linked to four events of host-switching in mammals".

This study is part of submission 11985 (Status: Published).

Analyses

Analysis 1

Analysis details

Name
Notes

Input data

1 Input object(s)

Analysis step

Phylogenetic inference --

Output data

2 Output object(s)

Analysis 2

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Phylogeny of Aspidoderidae Maximum Likelihood --

Output data

2 Output object(s)

Analysis 3

Analysis details

Input data

1 Input object(s)

Analysis step

Phylogeny of Aspidoderidae Parsimony --

Step details

Name

Software used

Name
Version
Algorithm
Commands
>Data file = rLSUAspido40gop10_OCT.nex >Heuristic search settings: > Optimality criterion = parsimony > Character-status summary: > Of 927 total characters: > All characters are of type 'unord' > All characters have equal weight > 284 characters are constant > 130 variable characters are parsimony-uninformative > Number of parsimony-informative characters = 513 > Gaps are treated as "missing" > Starting tree(s) obtained via stepwise addition > Addition sequence: simple (reference taxon = AM411622.1Toxo cati) > Number of trees held at each step during stepwise addition = 1 > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Initial 'MaxTrees' setting = 100 (will be auto-increased by 100) > Branches collapsed (creating polytomies) if maximum branch length is zero > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 33947 > Score of best tree(s) found = 1849 > Number of trees retained = 2 > Time used = 0.20 sec

Output data

1 Output object(s)

Analysis 4

Analysis details

Input data

1 Input object(s)

Analysis step

Phylogeny of Aspidoderidae Morphology --

Output data

2 Output object(s)

Analysis 5

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Phylogeny of Aspidoderidae Maximum Likelihood PAUP --

Step details

Name

Software used

Name
Version
Algorithm
Commands
[! >Data file = rLSUAspido40gop10_OCT.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > User-specified substitution rate matrix = > - 1.432300 3.663800 0.402300 > 1.432300 - 0.910700 2.143900 > 3.663800 0.910700 - 1.000000 > 0.402300 2.143900 1.000000 - > Assumed nucleotide frequencies (set by user): > A=0.27270 C=0.05460 G=0.20800 T=0.46470 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = 0.518 > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the GTR+G model > Number of distinct data patterns under this model = 601 > Molecular clock not enforced >Heuristic search completed > Total number of rearrangements tried = 8015 > Score of best tree(s) found = 8817.49099 > Number of trees retained = 1 > Time used = 00:45:28.2 ]

Output data