TreeBASE Search-Analyses for study 10433

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Analyses for Study 10433

Citation title: "Endophytes and potential pathogens of the baobab species Adansonia gregorii; a focus on the Botryosphaeriaceae ".

Study name: "Endophytes and potential pathogens of the baobab species Adansonia gregorii; a focus on the Botryosphaeriaceae ".

This study is part of submission 10423 (Status: Published).

Analyses

Analysis 1

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Heuristic search of ITS data set --

Step details

Name

Software used

Name
Version
Algorithm
Commands
Sequence data were analysed using Sequence Editor version 1.03 and sequences were manually aligned by inserting gaps. Gaps were treated as a fifth character and all characters were unordered and of equal weight. PAUP (Phylogenetic Analysis Using Parsimony) version 4.0b10 (Swofford, 2003) was used to determine phylogenetic relationships. The most parsimonious trees were found using heuristic searches, using stepwise addition and tree bisection and reconstruction (TBR) as the branch swapping algorithm. Branches were collapsed if maximum length was zero. Uninformative and ambiguous characters were excluded from analysis. 1000 replications were performed.

Output data

1 Output object(s)

Analysis 2

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Heuristic search of EF data set --

Step details

Name

Software used

Name
Version
Algorithm
Commands
Sequence data were analysed using Sequence Editor version 1.03 and sequences were manually aligned by inserting gaps. Gaps were treated as a fifth character and all characters were unordered and of equal weight. PAUP (Phylogenetic Analysis Using Parsimony) version 4.0b10 (Swofford, 2003) was used to determine phylogenetic relationships. The most parsimonious trees were found using heuristic searches, using stepwise addition and tree bisection and reconstruction (TBR) as the branch swapping algorithm. Branches were collapsed if maximum length was zero. Uninformative and ambiguous characters were excluded from analysis. 1000 replications were performed.

Output data

1 Output object(s)

Analysis 3

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Combined ITS and EF analysis --

Step details

Name

Software used

Name
Version
Algorithm
Commands
Parsimony analysis was performed on combined datasets in PAUP (Phylogenetic Analysis Using Parsimony) version 4.0b10 (Swofford 1999). Non-informative characters were removed prior to analysis and characters were unweighted and unordered. Characters were 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 (Hillis & Huelsenbeck 1992). Branch and branch node supports were determined using 1000 bootstrap replicates (Felsenstein 1985).

Output data

Analyses for Study 10433

Analyses

Analysis 1

1 Input object(s)

Heuristic search of ITS data set --

1 Output object(s)

Analysis 2

1 Input object(s)

Heuristic search of EF data set --

1 Output object(s)

Analysis 3

1 Input object(s)

Combined ITS and EF analysis --

2 Output object(s)