ADDITIONAL FILE 3: SOFTWARE AND SETTINGS FOR SUPERTREE ...

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Additional file 3

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Additional file 3

0.12. 0.06. 0.08. 0.06 0.10. 0.09. 0. 12 0.05. 0.09 0.27 0.17. 0.05. 0.20. 0.08. 0.17 ... 0.02. 0.11. 0.09. 0.02. 0.03. 0.08. 0.04. 0.30. 0.05. 0.07. 0.13. 0.07. 0.07. 0.14.

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secretory peroxidase [Catharanthus roseus]. 3E-80. CaF1_JIE_03_G_05 ...... Danio rerio partial mRNA for lecithin retinol acetyltransferase (lrat gene) 0.003.

ADDITIONAL FILE 3: SOFTWARE AND SETTINGS FOR SUPERTREE ...

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ADDITIONAL FILE 3: SOFTWARE AND SETTINGS FOR SUPERTREE. ANALYSIS. Method. Software. Settings other than defaults. Software author. (related ...

ADDITIONAL FILE 3: SOFTWARE AND SETTINGS FOR SUPERTREE ANALYSIS Method

Software

Standard MRP

PAUP* v. 4

MRC

MIX (PHYLIP v. 3.66)

Average Consensus Clann v. 3.0.2

Settings other than defaults Replicates = 100, addition sequence = random Replicates = 100, threshold = 2.0 (as for Ross & Rodrigo, 2004) -

Software author (related reference) Swofford (2002) Felsenstein (1989)

Creevey & McInerney (2005)

Creevey, C. & McInerney, J. O. 2005 Clann: investigating pylogenetic information through supertree analyses. Bioinformatics 21, 390-392. Felsenstein, J. 1989 PHYLIP -- Phylogeny Inference Package. Cladistics 5, 164-166. Swofford, D. L. 2002 PAUP*, Phylogenetic Analysis Using Parsimony (*and Other Methods). Sunderland: Sinauer.