TreeBASE Search-Analyses for study 10464

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Analyses for Study 10464

Citation title: "Pathogenic Botryosphaeriaceae associated with Mangifera indica in the Kimberley Region of Western Australia".

Study name: "Pathogenic Botryosphaeriaceae associated with Mangifera indica in the Kimberley Region of Western Australia".

This study is part of submission 10454 (Status: Published).

Analysis details

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Input data

Analysis step

Step details

Name

Software used

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Version
Algorithm
Commands
Parsimony analysis was performed on individual and combined datasets in PAUP (Phylogenetic Analysis Using Parsimony) version 4.0b10. Non-informative characters were removed prior to analysis and characters were and unordered and weighted according to the consistency index. The most parsimonious trees were obtained by using heuristic searches with random stepwise addition in 1000 replicates, with the tree bisection-reconnection branch-swapping option on and the steepest-descent option off. Branches of zero length were collapsed and all multiple equally parsimonious trees were saved. Estimated levels of homoplasy and phylogenetic signal (retention and consistency indices) were determined. Branch and branch node supports were determined using 1000 bootstrap replicates.

Output data

Analysis details

Input data

Analysis step

Step details

Name

Software used

Name
Version
Algorithm
Commands
Parsimony analysis was performed on individual in PAUP (Phylogenetic Analysis Using Parsimony) version 4.0b10. Non-informative characters were removed prior to analysis and characters were and unordered and unweighted. Characters we reweighted according to the consistency index.The most parsimonious trees were obtained by using heuristic searches with random stepwise addition in 1000 replicates, with the tree bisection-reconnection branch-swapping option on and the steepest-descent option off. Branches of zero length were collapsed and all multiple equally parsimonious trees were saved. Estimated levels of homoplasy and phylogenetic signal (retention and consistency indices) were determined. Branch and branch node supports were determined using 1000 bootstrap replicates.

Output data

Analysis details

Input data

Analysis step

Step details

Name

Software used

Name
Version
Algorithm
Commands
Parsimony analysis was performed on individual in PAUP (Phylogenetic Analysis Using Parsimony) version 4.0b10. Non-informative characters were removed prior to analysis and characters were and unordered and unweighted. Characters we reweighted according to the consistency index. The most parsimonious trees were obtained by using heuristic searches with random stepwise addition in 1000 replicates, with the tree bisection-reconnection branch-swapping option on and the steepest-descent option off. Branches of zero length were collapsed and all multiple equally parsimonious trees were saved. Estimated levels of homoplasy and phylogenetic signal (retention and consistency indices) were determined. Branch and branch node supports were determined using 100 bootstrap replicates.

Output data